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Sean,
Since one cannot update GLIBC without breaking the OS, are we now at a point where all Red Hat variants are no longer supported? You are supporting Macs and Windows now, but not the largest market share linux?
Both EL7 and EL6 have GLIBC < the required GLIBC-2.23, so is it the case that the hundreds of computers running RHEL6/RHEL7 variants are no longer able to use SeaDAS? (our university has a support agreement with Red Hat, and all our cluster operations (100s of machines), use the most current Red Hat EL6. These machines have literally hundreds of specialized custom compiled programs used by many many different research groups. The university cannot update to another distribution without expending enormous resources including breaking contracts, etc. And this affects all Red Hat, CentOS, Scientific linux and many other distros shown here:
https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives
And Red Hat is the market leader of Linux distributions, with an estimated market share of 67%!!! (Not sure if that includes variants).
Comments suggested that it can be recompiled from source, however, VIIRS is not open source code, and thus cannot be recompiled from source as none exists for distribution. If I use 7.4 to process VIIRS data, am I correct that I will not get updated LUTS? Have/will the LUTS changed for VIIRS in 7.5? If I don't update the code, I can never get new LUTS for terra modis regardless. And if I do recompile, I cannot process VIIRS which is a huge part of our business.
You mentioned in one place:
"Since you're in a CentOS world, you may be able to just build on the oldest system and run those binaries on all the machines."
However, it looks that is never going to work for VIIRS. We were able to use RHEL until now. Is it not possible that the SeaDAS group compiles SeaDAS 7.5 with compat libraries that can be used on the Red Hat variants (And others)? There isn't really an alternative that I can see right now. Our cluster has been down this week for updates to the GPFS file system alone (people from IBM are here now) so I would imagine, that changing everything for one program isn't going to happen. It would take compiling hundreds of programs.
https://en.wikipedia.org/wiki/IBM_General_Parallel_File_System
If I am missing something, please let me know.
Brock
Since one cannot update GLIBC without breaking the OS, are we now at a point where all Red Hat variants are no longer supported? You are supporting Macs and Windows now, but not the largest market share linux?
Both EL7 and EL6 have GLIBC < the required GLIBC-2.23, so is it the case that the hundreds of computers running RHEL6/RHEL7 variants are no longer able to use SeaDAS? (our university has a support agreement with Red Hat, and all our cluster operations (100s of machines), use the most current Red Hat EL6. These machines have literally hundreds of specialized custom compiled programs used by many many different research groups. The university cannot update to another distribution without expending enormous resources including breaking contracts, etc. And this affects all Red Hat, CentOS, Scientific linux and many other distros shown here:
https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives
And Red Hat is the market leader of Linux distributions, with an estimated market share of 67%!!! (Not sure if that includes variants).
Comments suggested that it can be recompiled from source, however, VIIRS is not open source code, and thus cannot be recompiled from source as none exists for distribution. If I use 7.4 to process VIIRS data, am I correct that I will not get updated LUTS? Have/will the LUTS changed for VIIRS in 7.5? If I don't update the code, I can never get new LUTS for terra modis regardless. And if I do recompile, I cannot process VIIRS which is a huge part of our business.
You mentioned in one place:
"Since you're in a CentOS world, you may be able to just build on the oldest system and run those binaries on all the machines."
However, it looks that is never going to work for VIIRS. We were able to use RHEL until now. Is it not possible that the SeaDAS group compiles SeaDAS 7.5 with compat libraries that can be used on the Red Hat variants (And others)? There isn't really an alternative that I can see right now. Our cluster has been down this week for updates to the GPFS file system alone (people from IBM are here now) so I would imagine, that changing everything for one program isn't going to happen. It would take compiling hundreds of programs.
https://en.wikipedia.org/wiki/IBM_General_Parallel_File_System
If I am missing something, please let me know.
Brock
Looks like I am in the same boat. I am on CentOS 7, with GLIBC 2.17.... I tried compiling from source as well. No luck. Stuck at Step 4 at https://seadas.gsfc.nasa.gov/build_ocssw/
[...]
Scanning dependencies of target H5test_FortranHavekind
[ 0%] Built target zip_perf_files
[ 0%] Building Fortran object fortran/src/CMakeFiles/H5test_FortranHavekind-shared.dir/H5test_kind_STORAGE_SIZE.f90.o
[ 0%] Building Fortran object fortran/src/CMakeFiles/H5test_FortranHavekind.dir/H5test_kind_STORAGE_SIZE.f90.o
[ 0%] Building C object src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o
[ 0%] Building C object src/CMakeFiles/H5detect.dir/H5detect.c.o
[ 0%] Linking C executable ../bin/H5make_libsettings
[ 0%] Linking Fortran executable ../../bin/H5test_FortranHavekind-shared
[ 0%] Linking Fortran executable ../../bin/H5test_FortranHavekind
[ 0%] Built target H5make_libsettings
[ 0%] Built target H5test_FortranHavekind-shared
[ 0%] Built target H5test_FortranHavekind
[ 0%] Generating ../H5fortran_detect.f90
/opt/seadas/seadas-7.5/ocssw/opt/src/hdf5/hdf5-1.8.18/build/bin/H5test_FortranHavekind: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by /opt/seadas/seadas-7.5/ocssw/opt/lib/libquadmath.so.0)
make[2]: *** [fortran/H5fortran_detect.f90] Error 1
make[2]: *** Deleting file `fortran/H5fortran_detect.f90'
make[1]: *** [fortran/src/CMakeFiles/H5fortran_detect.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 0%] Linking C executable ../bin/H5detect
[ 0%] Built target H5detect
make: *** [all] Error 2
***** make failed *****
***** BuildIt (hdf5) failed *****
If you have gcc-4; remove $OCSSWROOT/opt/lib/libquadmath.so.0 and try the binaries we distribute.
Sean
Sean
Brock,
We are under no obligation to make sure users can compile the source code we distribute.
We do not support building OCSSW under Windows - you'll notice our example uses Ubuntu
as a VM (or WSL option)
macOS is easy since it's generally up-to-date and we have the OS here to build against.
VIIRS is another ball of wax, a legal one we've been struggling with for 3 years - and continue to do so.
I still hold out hope that we can release the code to the public, but for now we cannot.
It is not my business what your business is, nor is it my business to ensure you can do your business.
The binaries we distribute support VIIRS, and are supported under freely available OSes.
All OSes? No. But ensuring it works on all OSes is not our business, nor do we have the resources to
make it our business.
While I understand your frustration, the reality is that our resources are limited and while we will help as we are able,
you get what you pay for.
BTW, another user, with Scientific Linux, was able - with very few minor modifications - to get the code to compile
...and his patches were included in the distribution this morning (oh, and those changes had nothing to do with GLIBC)
So, it's NOT all RH based OSes.
Sean
We are under no obligation to make sure users can compile the source code we distribute.
We do not support building OCSSW under Windows - you'll notice our example uses Ubuntu
as a VM (or WSL option)
macOS is easy since it's generally up-to-date and we have the OS here to build against.
VIIRS is another ball of wax, a legal one we've been struggling with for 3 years - and continue to do so.
I still hold out hope that we can release the code to the public, but for now we cannot.
It is not my business what your business is, nor is it my business to ensure you can do your business.
The binaries we distribute support VIIRS, and are supported under freely available OSes.
All OSes? No. But ensuring it works on all OSes is not our business, nor do we have the resources to
make it our business.
While I understand your frustration, the reality is that our resources are limited and while we will help as we are able,
you get what you pay for.
BTW, another user, with Scientific Linux, was able - with very few minor modifications - to get the code to compile
...and his patches were included in the distribution this morning (oh, and those changes had nothing to do with GLIBC)
So, it's NOT all RH based OSes.
Sean
I made a Virtual machine for CentOS 7 last night. Here is what I did.
Works fine without recompiling anything.
I am in the process of recompiling everything on CentOS 7. I'll get back to you with the results of that.
Hope that helps.
don
- Install CentOS 7
glibc version is 2.17
- $ yum group install "Development Tools"
This gives me gcc 4.8.5
- download https://oceandata.sci.gsfc.nasa.gov/ocssw/install_ocssw.py
- $ chmod +x install_ocssw.py
- $ install_ocssw.py -i ocssw -s --aqua
- $ export $OCSSWROOT=$HOME/ocssw
- $ source $OCSSWROOT/OCSSW_bash.env
- $ rm $OCSSWROOT/opt/lib/libquadmath.so.0
The "Development Tools" supplies a compatable version
- grab an AQUA L1A file
- $ modis_GEO.py A2018101191500.L1A_LAC
- $ modis_L1B.py A2018101191500.L1A_LAC
- $ l2gen ifile=A2018101191500L1B_LAC geofile=A2018101191500.GEO ofile=A2018101191500.L2
Works fine without recompiling anything.
I am in the process of recompiling everything on CentOS 7. I'll get back to you with the results of that.
Hope that helps.
don
Don,
Thanks. I was able to follow Sean's advice and:
rm $OCSSWROOT/opt/lib/libquadmath.so.0
But I'm happy that you tell me:
"The "Development Tools" supplies a compatable version"
And this worked in RHEL7, however, this seems not to help at all for RHEL6 machines:
[oo_processing@seadog ~]$ which l2gen
/optics1/software/seadas/seadas-7.5/ocssw/bin/l2gen
[oo_processing@seadog ~]$ l2gen -h
l2gen: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by l2gen)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l2gen)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libmfhdf.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libdf.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdf.so.11)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libhdf5.so.10.2.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgsl.so.19)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libhdf5_hl.so.10.2.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libproj.so.9)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgeotiff.so.2)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libtiff.so.5)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libpugixml.so.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libfann.so.2)
l2gen: /lib64/libm.so.6: version `GLIBC_2.15' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libopenjp2.so.7)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libopenjp2.so.7)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdf_c++4.so.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdff.so.6)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgfortran.so.3)
l2gen: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgfortran.so.3)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/../lib/libxdr.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/../lib/libjpeg.so.9)
WHERE:
gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)
Further, if I understand Sean correctly, if you recompile everything on CentOS7, you will not have the ability to use VIIRS processing.
The biggest issue I face is that I need to run the OCSSW code on a huge cluster with hundreds of machines, but they are all RHEL6. Is there any way you can compile the VIIRS in a CentOS6 virtual machine?
Brock
Thanks. I was able to follow Sean's advice and:
rm $OCSSWROOT/opt/lib/libquadmath.so.0
But I'm happy that you tell me:
"The "Development Tools" supplies a compatable version"
And this worked in RHEL7, however, this seems not to help at all for RHEL6 machines:
[oo_processing@seadog ~]$ which l2gen
/optics1/software/seadas/seadas-7.5/ocssw/bin/l2gen
[oo_processing@seadog ~]$ l2gen -h
l2gen: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by l2gen)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l2gen)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libmfhdf.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libdf.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdf.so.11)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libhdf5.so.10.2.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgsl.so.19)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libhdf5_hl.so.10.2.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libproj.so.9)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgeotiff.so.2)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libtiff.so.5)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libpugixml.so.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libfann.so.2)
l2gen: /lib64/libm.so.6: version `GLIBC_2.15' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libopenjp2.so.7)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libopenjp2.so.7)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdf_c++4.so.1)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libnetcdff.so.6)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgfortran.so.3)
l2gen: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/libgfortran.so.3)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/../lib/libxdr.so.0)
l2gen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /optics1/software/seadas/seadas-7.5/ocssw/bin/../opt/lib/../lib/libjpeg.so.9)
WHERE:
gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)
Further, if I understand Sean correctly, if you recompile everything on CentOS7, you will not have the ability to use VIIRS processing.
The biggest issue I face is that I need to run the OCSSW code on a huge cluster with hundreds of machines, but they are all RHEL6. Is there any way you can compile the VIIRS in a CentOS6 virtual machine?
Brock
OK, I compiled everything...
Using Virtual Machine with CentOS 7 above
- grab latest cmake binaries, install and get the new cmake into your PATH
- $ yum install libX11-devl.x86_64
- $ cd ocssw/opt/src
- $ ./BuildIt
- $ cd ../../ocssw-src
- $ mkdir build; cd build; cmake ..
- $ make -j 20 install
all works fine.
Using Virtual Machine with CentOS 7 above
- grab latest cmake binaries, install and get the new cmake into your PATH
- $ yum install libX11-devl.x86_64
- $ cd ocssw/opt/src
- $ ./BuildIt
- $ cd ../../ocssw-src
- $ mkdir build; cd build; cmake ..
- $ make -j 20 install
all works fine.
Actually, we put precompiled VIIRS libs in ocssw/opt/lib, so you can compile and still have VIIRS functionality. You need to use gcc-4.x since the C++ ABI changed at gcc-5.x
you need to edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
you need to edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
Note that my RHEL6 machines run gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)
Will this work since you state:
"You need to use gcc-4.x since the C++ ABI changed at gcc-5.x"
BTW, how did you get around the hdf5 require cmake3?
Will this work since you state:
"You need to use gcc-4.x since the C++ ABI changed at gcc-5.x"
BTW, how did you get around the hdf5 require cmake3?
We'll see how this plays out on CentOS 6. Before the release we made sure everything worked on CentOS 7.
I just grabbed the latest binaries from cmake.org and installed them in my home dir.
don
I just grabbed the latest binaries from cmake.org and installed them in my home dir.
don
Don,
It seems CentOS 6, not so much.
I installed a CentOS 6.9 virtual machine and a new version of cmake and git into a virtual CentOS6 machine.
NOTE THAT
$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
And it is within the gcc-4.x you specified.
This is where it errors out:
$ ./install_ocssw.py --install-dir=$INSTALL_DIR/ocssw --git-branch=v7.5 --src
Installing bundles.sha256sum (1 of 9)
--2018-05-13 14:09:17-- https://oceandata.sci.gsfc.nasa.gov/ocssw/bundles.sha256sum
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3570 (3.5K) [application/octet-stream]
Saving to: “bundles.sha256sum”
100%[===================================================================================>] 3,570 --.-K/s in 0s
2018-05-13 14:09:18 (259 MB/s) - “bundles.sha256sum” saved [3570/3570]
Installing common (2 of 9)
Installing OCSSW_bash.env (3 of 9)
--2018-05-13 14:09:19-- https://oceandata.sci.gsfc.nasa.gov/ocssw/OCSSW_bash.env.v7.5
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.`GLIBC_2.14'
HTTP request sent, awaiting response... 200 OK
Length: 3001 (2.9K) [application/octet-stream]
Saving to: “OCSSW_bash.env.v7.5”
100%[===================================================================================>] 3,001 --.-K/s in 0s
2018-05-13 14:09:19 (210 MB/s) - “OCSSW_bash.env.v7.5” saved [3001/3001]
Installing ocrvc (4 of 9)
Installing bin (5 of 9)
Installing opt (6 of 9)
Installing src (7 of 9)
Installing opt-src (8 of 9)
--2018-05-13 14:09:23-- https://oceandata.sci.gsfc.nasa.gov/ocssw/opt-src-v7.5.tar
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 229611520 (219M) [application/octet-stream]
Saving to: “opt-src-v7.5.tar”
100%[===================================================================================>] 229,611,520 11.9M/s in 17s
2018-05-13 14:09:41 (12.6 MB/s) - “opt-src-v7.5.tar” saved [229611520/229611520]
Installing scripts (9 of 9)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libmfhdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libxdr.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libjpeg.so.9)
Error - Can not run an installed executable
CentOS 6 has GLIBC_2.12, CentOS 7 has GLIBC_2.17 and thus works, is my guess.
Any ideas are appreciated as I must make this work on a Redhat 6 cluster. If those `GLIBC_2.14' compiled libs were compiled with GLIBC_2.12, I might stand a chance.
Thanks,
Brock
It seems CentOS 6, not so much.
I installed a CentOS 6.9 virtual machine and a new version of cmake and git into a virtual CentOS6 machine.
NOTE THAT
$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
And it is within the gcc-4.x you specified.
This is where it errors out:
$ ./install_ocssw.py --install-dir=$INSTALL_DIR/ocssw --git-branch=v7.5 --src
Installing bundles.sha256sum (1 of 9)
--2018-05-13 14:09:17-- https://oceandata.sci.gsfc.nasa.gov/ocssw/bundles.sha256sum
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3570 (3.5K) [application/octet-stream]
Saving to: “bundles.sha256sum”
100%[===================================================================================>] 3,570 --.-K/s in 0s
2018-05-13 14:09:18 (259 MB/s) - “bundles.sha256sum” saved [3570/3570]
Installing common (2 of 9)
Installing OCSSW_bash.env (3 of 9)
--2018-05-13 14:09:19-- https://oceandata.sci.gsfc.nasa.gov/ocssw/OCSSW_bash.env.v7.5
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.`GLIBC_2.14'
HTTP request sent, awaiting response... 200 OK
Length: 3001 (2.9K) [application/octet-stream]
Saving to: “OCSSW_bash.env.v7.5”
100%[===================================================================================>] 3,001 --.-K/s in 0s
2018-05-13 14:09:19 (210 MB/s) - “OCSSW_bash.env.v7.5” saved [3001/3001]
Installing ocrvc (4 of 9)
Installing bin (5 of 9)
Installing opt (6 of 9)
Installing src (7 of 9)
Installing opt-src (8 of 9)
--2018-05-13 14:09:23-- https://oceandata.sci.gsfc.nasa.gov/ocssw/opt-src-v7.5.tar
Resolving oceandata.sci.gsfc.nasa.gov... 169.154.128.84, 2001:4d0:2418:128::84
Connecting to oceandata.sci.gsfc.nasa.gov|169.154.128.84|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 229611520 (219M) [application/octet-stream]
Saving to: “opt-src-v7.5.tar”
100%[===================================================================================>] 229,611,520 11.9M/s in 17s
2018-05-13 14:09:41 (12.6 MB/s) - “opt-src-v7.5.tar” saved [229611520/229611520]
Installing scripts (9 of 9)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libmfhdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/libdf.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libxdr.so.0)
hdp: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/bin/../lib/../lib/libjpeg.so.9)
Error - Can not run an installed executable
CentOS 6 has GLIBC_2.12, CentOS 7 has GLIBC_2.17 and thus works, is my guess.
Any ideas are appreciated as I must make this work on a Redhat 6 cluster. If those `GLIBC_2.14' compiled libs were compiled with GLIBC_2.12, I might stand a chance.
Thanks,
Brock
- install CentOS 6 "Software Development Workstation"
- install cmake 3.11
The binaries from cmake.org work fine.
- install a recent version of git > 2
- get newer compiler
$ yum install centos-release-scl
$ install devtoolset-4
$ scl enable devtoolset-4 bash
- get the source directories
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* lib
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
- this will get you everything except VIIRS. I have a few ideas to
make the old LIBC work.
- install cmake 3.11
The binaries from cmake.org work fine.
- install a recent version of git > 2
- get newer compiler
$ yum install centos-release-scl
$ install devtoolset-4
$ scl enable devtoolset-4 bash
- get the source directories
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* lib
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
- this will get you everything except VIIRS. I have a few ideas to
make the old LIBC work.
I followed your directions to the letter from the virtual install of CentOS 6 "Software Development Workstation", and want to note the small difference in the install process:
#NOTE: the EOS and examples directories do not exist after running all_ocssw.py -i ocssw -s
#[bmurch@centos69 Seadas-7.5]$ cd /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/
#[bmurch@centos69 opt]$ ll
#total 28
#drwxrwxr-x. 2 bmurch bmurch 4096 May 14 10:41 bin
#drwxrwxr-x. 7 bmurch bmurch 4096 May 14 10:41 include
#drwxrwxr-x. 4 bmurch bmurch 12288 May 14 10:41 lib
#drwxrwxr-x. 9 bmurch bmurch 4096 May 14 10:41 share
#drwxrwxr-x. 32 bmurch bmurch 4096 Mar 22 13:30 src\
Perhaps you had EOS and examples from before?
make -j 20 install finished without errors.
ALL THE ONES THAT HAVE VIIRS IN THE NAME FAIL AS EXPECTED.
# EG
[bmurch@centos69 build]$ /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs --help
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs)
# HOWEVER MANY OTHER BINARIES FAIL AS WELL. DID YOU TEST THE BINARIES BELOW? See:
[bmurch@centos69 build]$ l1agen_seawifs --help
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)
[bmurch@centos69 bin]$ fixrgb
Segmentation fault (core dumped)
[bmurch@centos69 bin]$ interp_hycom_ascii
interp_hycom_ascii: error while loading shared libraries: libnetcdff.so.5: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ l0cnst_read_modis
l0cnst_read_modis: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0cnst_read_modis)
[bmurch@centos69 bin]$ l0info_seawifs
l0info_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0info_seawifs)
[bmurch@centos69 bin]$ l0regen_seawifs
l0regen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0regen_seawifs)
[bmurch@centos69 bin]$ l1agen_seawifs
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by l1agen_seawifs)
l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1agen_seawifs)
[bmurch@centos69 bin]$ l1info_aquarius
l1info_aquarius: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ l2bin_aquarius
l2bin_aquarius: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ landbin
landbin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landbin)
[bmurch@centos69 bin]$ landtimebin
landtimebin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landtimebin)
[bmurch@centos69 bin]$ mk_aquarius_ancillary_data
mk_aquarius_ancillary_data: error while loading shared libraries: libhdf5_fortran.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ oisst_info
oisst_info: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by oisst_info)
[bmurch@centos69 bin]$ smigen
smigen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by smigen)
[bmurch@centos69 bin]$ solar_xray
solar_xray: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ swh
swh: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ tec
tec: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
#NOTE: the EOS and examples directories do not exist after running all_ocssw.py -i ocssw -s
#[bmurch@centos69 Seadas-7.5]$ cd /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/opt/
#[bmurch@centos69 opt]$ ll
#total 28
#drwxrwxr-x. 2 bmurch bmurch 4096 May 14 10:41 bin
#drwxrwxr-x. 7 bmurch bmurch 4096 May 14 10:41 include
#drwxrwxr-x. 4 bmurch bmurch 12288 May 14 10:41 lib
#drwxrwxr-x. 9 bmurch bmurch 4096 May 14 10:41 share
#drwxrwxr-x. 32 bmurch bmurch 4096 Mar 22 13:30 src\
Perhaps you had EOS and examples from before?
make -j 20 install finished without errors.
ALL THE ONES THAT HAVE VIIRS IN THE NAME FAIL AS EXPECTED.
# EG
[bmurch@centos69 build]$ /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs --help
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1aextract_viirs)
# HOWEVER MANY OTHER BINARIES FAIL AS WELL. DID YOU TEST THE BINARIES BELOW? See:
[bmurch@centos69 build]$ l1agen_seawifs --help
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)
/home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/bmurch/Programming/Seadas/Seadas-7.5/ocssw/bin/l1agen_seawifs)
[bmurch@centos69 bin]$ fixrgb
Segmentation fault (core dumped)
[bmurch@centos69 bin]$ interp_hycom_ascii
interp_hycom_ascii: error while loading shared libraries: libnetcdff.so.5: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ l0cnst_read_modis
l0cnst_read_modis: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0cnst_read_modis)
[bmurch@centos69 bin]$ l0info_seawifs
l0info_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0info_seawifs)
[bmurch@centos69 bin]$ l0regen_seawifs
l0regen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l0regen_seawifs)
[bmurch@centos69 bin]$ l1agen_seawifs
l1agen_seawifs: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by l1agen_seawifs)
l1agen_seawifs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1agen_seawifs)
[bmurch@centos69 bin]$ l1info_aquarius
l1info_aquarius: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ l2bin_aquarius
l2bin_aquarius: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ landbin
landbin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landbin)
[bmurch@centos69 bin]$ landtimebin
landtimebin: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by landtimebin)
[bmurch@centos69 bin]$ mk_aquarius_ancillary_data
mk_aquarius_ancillary_data: error while loading shared libraries: libhdf5_fortran.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ oisst_info
oisst_info: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by oisst_info)
[bmurch@centos69 bin]$ smigen
smigen: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by smigen)
[bmurch@centos69 bin]$ solar_xray
solar_xray: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ swh
swh: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
[bmurch@centos69 bin]$ tec
tec: error while loading shared libraries: libhdf5.so.10.1.0: cannot open shared object file: No such file or directory
Those binaries are not build by default, so unless you modified your CMake configuration to include building them, you've still got the binaries we distributed.
BTW, you very likely don't need any of them anyway, so probably not worth your effort to rebuild them.
But so you'll believe me:
l1agen_seawifs is used to generate a SeaWiFS L1A file from a L0 file. SeaWiFS is dead....no more L0 data coming down.
Similary vestigial are l0info_seawifs and l0regen_seawifs.
fixrgb is so unnecessary not worth mentioning, but so you don't feel the need to ask - SeaWiFS True Color browse images could sometimes have pink or blue stripes with bad input data - this "fixed" those.
l0cnst_read_modis - just not needed, unless you REALLY want to read a MODIS L0 constructor file...trust me, you don't care.
The same is true of oisst_info (but for OISST files)
These: l1info_aquarius, l2bin_aquarius, mk_aquarius_ancillary_data, solar_xray, swh, tec, and interp_hycom_ascii
are all for Aquarius processing (both data and ancillary generation - something I really doubt you have a need to do.)
landbin and landtimebin are dead wood from the wayback machine of SeaWiFS Land processing. Both are superseded by l2bin/l3bin/l3mapgen now
smigen - replaced by l3mapgen
Long story short - there are a LOT of things we have or had programs for that are not terribly useful to the SeaDAS user community - these you can ignore
Sean
BTW, you very likely don't need any of them anyway, so probably not worth your effort to rebuild them.
But so you'll believe me:
l1agen_seawifs is used to generate a SeaWiFS L1A file from a L0 file. SeaWiFS is dead....no more L0 data coming down.
Similary vestigial are l0info_seawifs and l0regen_seawifs.
fixrgb is so unnecessary not worth mentioning, but so you don't feel the need to ask - SeaWiFS True Color browse images could sometimes have pink or blue stripes with bad input data - this "fixed" those.
l0cnst_read_modis - just not needed, unless you REALLY want to read a MODIS L0 constructor file...trust me, you don't care.
The same is true of oisst_info (but for OISST files)
These: l1info_aquarius, l2bin_aquarius, mk_aquarius_ancillary_data, solar_xray, swh, tec, and interp_hycom_ascii
are all for Aquarius processing (both data and ancillary generation - something I really doubt you have a need to do.)
landbin and landtimebin are dead wood from the wayback machine of SeaWiFS Land processing. Both are superseded by l2bin/l3bin/l3mapgen now
smigen - replaced by l3mapgen
Long story short - there are a LOT of things we have or had programs for that are not terribly useful to the SeaDAS user community - these you can ignore
Sean
I installed SeaDAS on my CentOS 7 server with glibc 2.17 as:
./install_ocssw.py --install-dir=./ocssw --git-branch=v7.5 --aqua --seawifs
then removed $OCSSWROOT/opt/lib/libquadmath.so.0 as Sean suggested and it seems to be working! So no need to compile from source! (only tested l3mapgen and l2gen).
Thanks Sean!
./install_ocssw.py --install-dir=./ocssw --git-branch=v7.5 --aqua --seawifs
then removed $OCSSWROOT/opt/lib/libquadmath.so.0 as Sean suggested and it seems to be working! So no need to compile from source! (only tested l3mapgen and l2gen).
Thanks Sean!
Don,
I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the make -j 20 install it fails. See below on VIIRS:
[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON) in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the make -j 20 install it fails. See below on VIIRS:
[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON) in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
Don,
I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the "make -j 20 install" it fails. SEE PART I.
"SEE PART II" very bottom below for errors when instructions followed exclude the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
PART I
[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON) in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
PART II
When I try it without making this change:
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
It builds fine, and the "$ make -j 20 install" install works fine.
BUT, only one viirs binary seems to work.
[bmurch@optics0 bin]$ ls *viirs*
calibrate_viirs geolocate_viirs l1aextract_viirs l2bin_viirs viirs_obc
[bmurch@optics0 bin]$ calibrate_viirs
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by calibrate_viirs)
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by calibrate_viirs)
[bmurch@optics0 bin]$ geolocate_viirs
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by geolocate_viirs)
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by geolocate_viirs)
[bmurch@optics0 bin]$ l1aextract_viirs
l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1aextract_viirs)
[bmurch@optics0 bin]$ viirs_obc
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by viirs_obc)
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by viirs_obc)
[bmurch@optics0 bin]$ l2bin_viirs
L2BIN_VIIRS 2.2.13 (May 18 2015 09:12:42)
This is version 2.2.13 of l2bin_viirs (compiled on May 18 2015 09:12:42)
Usage: l2bin_viirs parfile=parfile or
infile=infile ofile=ofile [sday=sday] [eday=eday]
resolve=resolve [flaguse=flaguse] [l3bprod=l3bprod]
[prodtype=prodtype] [noext=noext]
[rowgroup=rowgroup] [night=night]
parfile = parameter filename
infile = input filename/filelist
ofile = output bin filename
sday = start datadate (YYYYDDD) [ignored for "regional" prodtype]
eday = end datadate (YYYYDDD) [ignored for "regional" prodtype]
resolve = bin resolution (H,1,2,4,9,36)
flaguse = flags masked [see /SENSOR/l2bin_defaults.par]
l3bprod = bin products [default=all products]
Set to "ALL" or "all" for all L2 products in 1st input file.
Use ':' or ',' or ' ' as delimiters.
Use ';' or '=' to delineate minimum values.
prodtype = product type (Set to "regional" to bin all scans.) [default=day]
noext = set to 1 to suppress generation of external files
[default=0, (1 for "regional" prodtype)]
rowgroup = # of bin rows to process at once.
night = set to 1 for SST night processing [default=0]
qual_max = maximum acceptable quality [default=2]
verbose = Allow more verbose screen messages [default=0]
I am trying to get the code to install on my RHEL 6 cluster. It builds fine, but when I do the "make -j 20 install" it fails. SEE PART I.
"SEE PART II" very bottom below for errors when instructions followed exclude the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
PART I
[bmurch@optics0 build]$ gcc --version
gcc (GCC) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[bmurch@optics0 build]$ cmake --version
cmake version 3.7.1
CMake suite maintained and supported by Kitware (kitware.com/cmake).
$ install_ocssw.py -i ocssw -s
script fails at the end running "hdp" as a sanity test, but src is installed
$ export OCSSWROOT=~/ocssw
$ source $OCSSWROOT/OCSSW_bash.env
$ cd $OCSSWROOT/opt
$ rm -rf EOS bin examples include lib share
- openjpg seemed to behave strangly, so need to fix it.
edit $OCSSWROOT/opt/src/openjpeg/BuildIt
add "-DBUILD_THIRDPARTY=ON" to the cmake line in the BuildIt script
From:
https://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?pid=37368#pid37368
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
grep "Build VIIRS L1 code" $OCSSWROOT/ocssw-src/CMakeLists.txt
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
- OK build the third party libs
$ cd $OCSSWROOT/opt/src
$ ./BuildIt
- some libs get stuffed into a lib64 directory. Move them.
$ cd $OCSSWROOT/opt
$ mv lib64/* libll $OCC
$ mv lib64/cmake/* lib/cmake
$ mv lib64/pkgconfig/* lib/pkgconfig
- build OCSSW
$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..
$ make -j 20 install
goes though everything until I get to the make.
which seems to FAIL as it cannot find the viirs directories even with the OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON) in the ocssw/ocssw-src/CMakeLists.txt file. Errors here:
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
[ 33%] Linking Fortran executable l2bin
...
[ 33%] Building C object src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_mos_hdf.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/lonlat2pixline.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
...
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 34%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_ocm2_hdf.c.o
...
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1b_viirs_nc.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1bgen_generic.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building C object src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o
...
[ 36%] Linking CXX static library libbin++.a
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Linking CXX executable l3bin64
...
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 36%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/raygetpol.f.o
[ 36%] Built target l3bin64
[ 37%] Building Fortran object src/l2gen/CMakeFiles/l1info.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/xcal.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/get_f0.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/atmocor1_land.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1info.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/whitecaps.c.o
...
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_octs_hdf.c.o
make[2]: *** No rule to make target `/shares/cms_optics/apps/seadas/ocssw/opt/lib/libViirsCal.a', needed by `src/l2gen/l2binmatch64'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 37%] Building C object src/l2gen/CMakeFiles/l2binmatch64.dir/elev.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/b128_box_num.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/read_mask.c.o
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/l1_czcs_hdf.c.o
make[1]: *** [src/l2gen/CMakeFiles/l1info.dir/all] Error 2
[ 37%] Building C object src/l2gen/CMakeFiles/l1mapgen.dir/ll2vec.c.o
...
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l2binmatch64.dir/all] Error 2
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/airmass_avhrr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_hdf_generic_read.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_nc_generic_read.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 38%] Building Fortran object src/l2gen/CMakeFiles/l1mapgen.dir/avhrrsub5h.f.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_generic_write.c.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_mos_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_octs_hdf.c.o
[ 38%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1_czcs_hdf.c.o
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ll2vec.c.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/l1a_seawifs.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/etbpsub.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building C object src/l2gen/CMakeFiles/l1brsgen.dir/ftrim.c.o
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/hmf8.f.o
make[1]: *** [src/l2gen/CMakeFiles/l1mapgen.dir/all] Error 2
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/lenstr.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/raygetpol.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/simpsn.f.o
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
[ 39%] Building Fortran object src/l2gen/CMakeFiles/l1brsgen.dir/airmass_avhrr.f.o
/shares/cms_optics/apps/seadas/ocssw/ocssw-src/src/l2gen/l1_viirs_nc.c:12:39: fatal error: Calibrate_Viirs_Connector.h: No such file or directory
#include <Calibrate_Viirs_Connector.h>
^
compilation terminated.
make[2]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/l1_viirs_nc.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCal"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/ViirsCmn"
Warning: Nonexistent include directory "/shares/cms_optics/apps/seadas/ocssw/opt/include/novas"
make[1]: *** [src/l2gen/CMakeFiles/l1brsgen.dir/all] Error 2
make: *** [all] Error 2
PART II
When I try it without making this change:
edit ocssw/ocssw-src/CMakeLists.txt line 29
OPTION(BUILD_VIIRS_L1 "Build VIIRS L1 code" ON)
It builds fine, and the "$ make -j 20 install" install works fine.
BUT, only one viirs binary seems to work.
[bmurch@optics0 bin]$ ls *viirs*
calibrate_viirs geolocate_viirs l1aextract_viirs l2bin_viirs viirs_obc
[bmurch@optics0 bin]$ calibrate_viirs
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by calibrate_viirs)
calibrate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by calibrate_viirs)
[bmurch@optics0 bin]$ geolocate_viirs
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by geolocate_viirs)
geolocate_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by geolocate_viirs)
[bmurch@optics0 bin]$ l1aextract_viirs
l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by l1aextract_viirs)
[bmurch@optics0 bin]$ viirs_obc
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by viirs_obc)
viirs_obc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by viirs_obc)
[bmurch@optics0 bin]$ l2bin_viirs
L2BIN_VIIRS 2.2.13 (May 18 2015 09:12:42)
This is version 2.2.13 of l2bin_viirs (compiled on May 18 2015 09:12:42)
Usage: l2bin_viirs parfile=parfile or
infile=infile ofile=ofile [sday=sday] [eday=eday]
resolve=resolve [flaguse=flaguse] [l3bprod=l3bprod]
[prodtype=prodtype] [noext=noext]
[rowgroup=rowgroup] [night=night]
parfile = parameter filename
infile = input filename/filelist
ofile = output bin filename
sday = start datadate (YYYYDDD) [ignored for "regional" prodtype]
eday = end datadate (YYYYDDD) [ignored for "regional" prodtype]
resolve = bin resolution (H,1,2,4,9,36)
flaguse = flags masked [see /SENSOR/l2bin_defaults.par]
l3bprod = bin products [default=all products]
Set to "ALL" or "all" for all L2 products in 1st input file.
Use ':' or ',' or ' ' as delimiters.
Use ';' or '=' to delineate minimum values.
prodtype = product type (Set to "regional" to bin all scans.) [default=day]
noext = set to 1 to suppress generation of external files
[default=0, (1 for "regional" prodtype)]
rowgroup = # of bin rows to process at once.
night = set to 1 for SST night processing [default=0]
qual_max = maximum acceptable quality [default=2]
verbose = Allow more verbose screen messages [default=0]
Actually, Sean, one of my issues was with libquadmath.so.
To compile on SL7.3, I went to opt and mv lib lib.save, mv bin bin.save (as you'll need this later!).
Then I rebuilt the 3rd party stuff. Only issue I had was that puixml, liblapack, ..., which installed in a 'lib64' instead of 'lib'. So, I just moved them.
Then in opt/lib, you need copy the libViirs*a static libraries since the code to build them does not exist. Also libnovas.a.
Once I had the 3rd party stuff recompiled, I was able to rebuild OCSSW (mkdir build, cd build, cmake .., make). I had two minor fixes that Sean has evidently pushed.
Paul
To compile on SL7.3, I went to opt and mv lib lib.save, mv bin bin.save (as you'll need this later!).
Then I rebuilt the 3rd party stuff. Only issue I had was that puixml, liblapack, ..., which installed in a 'lib64' instead of 'lib'. So, I just moved them.
Then in opt/lib, you need copy the libViirs*a static libraries since the code to build them does not exist. Also libnovas.a.
Once I had the 3rd party stuff recompiled, I was able to rebuild OCSSW (mkdir build, cd build, cmake .., make). I had two minor fixes that Sean has evidently pushed.
Paul
I put up a new web page with a link to the VIIRS libs you need to compile on CentOS 6.
This page also describs running and compiling on CentOS 7
https://seadas.gsfc.nasa.gov/build_ocssw/rhel/
don
This page also describs running and compiling on CentOS 7
https://seadas.gsfc.nasa.gov/build_ocssw/rhel/
don
Don
Thanks so much.
I was able to compile with the viirs tar.
However, not having done this before with OCSSW, I suspect I'm missing something.
When I tried this:
geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO
it came back with an error: "Can't open parameter file - $OCSSWROOT/share/viirs/npp/instrument_default"
Then I remembered the DEM files too, so I grabbed them and when I tried to install them, I noticed that there was no $OCSSWROOT/share/viirs directory.
So I thought I needed to "install_opcssw.py --viirs" and it went and git everything (Bundles 1 - 10) failing on 9. Is there some way to exclude some of these bundles? I modify the OCSSW_bash.env, and it is overwritten every time (as well as modifications to other files eg: HiRES=1) are overwritten. Does this flag function in that way: --no-update
"geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO" now returns all the GLIBC 2.14/17 symbol errors
Alas, what am I missing? I usually use the GUI to install the individuals like MODIST, MODISA, OLCI .... Obviously that won't work.
Should I be installing everything (all sensors) first (to get all the proper directories and files) and then install the source, and then follow the directions https://seadas.gsfc.nasa.gov/build_ocssw/rhel/ again?
Or something like this:
./install_ocssw.py -v -c --src --aquarius --avhrr --czcs --goci --hico --meris --aqua --terra --mos --msi --ocm1 --ocm2 --octs --olcis3a --oli --osmi --seawifs --viirsn --viirsj1
And then the CentOS6 source build?
And most importantly, what should I be doing in the future so that I don't mess things up with a git of files that are not good for the CentOS6 boxes?
Thanks,
Brock
Thanks so much.
I was able to compile with the viirs tar.
However, not having done this before with OCSSW, I suspect I'm missing something.
When I tried this:
geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO
it came back with an error: "Can't open parameter file - $OCSSWROOT/share/viirs/npp/instrument_default"
Then I remembered the DEM files too, so I grabbed them and when I tried to install them, I noticed that there was no $OCSSWROOT/share/viirs directory.
So I thought I needed to "install_opcssw.py --viirs" and it went and git everything (Bundles 1 - 10) failing on 9. Is there some way to exclude some of these bundles? I modify the OCSSW_bash.env, and it is overwritten every time (as well as modifications to other files eg: HiRES=1) are overwritten. Does this flag function in that way: --no-update
"geolocate_viirs v ifile=V2018137192400.L1A_SNPP.nc geofile_mod=V20181371942.GEO" now returns all the GLIBC 2.14/17 symbol errors
Alas, what am I missing? I usually use the GUI to install the individuals like MODIST, MODISA, OLCI .... Obviously that won't work.
Should I be installing everything (all sensors) first (to get all the proper directories and files) and then install the source, and then follow the directions https://seadas.gsfc.nasa.gov/build_ocssw/rhel/ again?
Or something like this:
./install_ocssw.py -v -c --src --aquarius --avhrr --czcs --goci --hico --meris --aqua --terra --mos --msi --ocm1 --ocm2 --octs --olcis3a --oli --osmi --seawifs --viirsn --viirsj1
And then the CentOS6 source build?
And most importantly, what should I be doing in the future so that I don't mess things up with a git of files that are not good for the CentOS6 boxes?
Thanks,
Brock
Don,
Are there a couple of things left out of the VIIRS build? I have issued this command:
./install_ocssw.py -v -c -i ocssw --src --aquarius --avhrr --czcs --goci --hico --meris --aqua --terra --mos --msi --ocm1 --ocm2 --octs --olcis3a --oli --osmi --seawifs --viirsn --viirsj1
On both a clean CentOS6 virtual machine and a clean RHEL6 cluster environment. Followed directions https://seadas.gsfc.nasa.gov/build_ocssw/rhel/
In both cases everything appeared to build correctly.
However, this is what I see in the bin dir:
[oo_processing@optics0 bin]$ ll *viirs*
cms_optics 936820 May 21 14:57 calibrate_viirs
cms_optics 925261 May 21 14:57 geolocate_viirs
cms_optics 155624 May 21 14:19 l1aextract_viirs
cms_optics 7299556 May 21 14:19 l2bin_viirs
cms_optics 728728 May 21 14:19 viirs_obc
NOTE that the two files (calibrate_viirs and geolocate_viirs) were compiled (see time stamps) and work. l2bin_viirs was not compiled, but it seems to work without compiling.
BUT these two files (not built) still error out:
[oo_processing@optics0 bin]$ ./l1aextract_viirs
./l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./l1aextract_viirs)
[oo_processing@optics0 bin]$ ./viirs_obc
./viirs_obc: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by ./viirs_obc)
./viirs_obc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./viirs_obc)
l1aextract_viirs is the first program I use in my VIIRS processing.
In fact, here is the bin dir: 14:19 is when I did the ./install_ocssw.py and anything after 14:56 in BOLD is newly compiled)
[oo_processing@optics0 bin]$ ll -ltr
total 80128
cms_optics 8848 May 21 14:19 fixrgb
cms_optics 155624 May 21 14:19 l1aextract_viirs
cms_optics 14 May 21 14:19 l1bgen -> l1bgen_generic
cms_optics 7299556 May 21 14:19 l2bin_viirs
cms_optics 309648 May 21 14:19 smigen
cms_optics 27928 May 21 14:19 smitoppm
cms_optics 728728 May 21 14:19 viirs_obc
cms_optics 17872 May 21 14:19 bindepths
cms_optics 44848 May 21 14:19 biosmap
cms_optics 71880 May 21 14:19 interp_hycom_ascii
cms_optics 105256 May 21 14:19 l0cnst_read_modis
cms_optics 32336 May 21 14:19 l0info_seawifs
cms_optics 22304 May 21 14:19 l0regen_seawifs
cms_optics 439800 May 21 14:19 l1agen_seawifs
cms_optics 165953 May 21 14:19 l1info_aquarius
cms_optics 854350 May 21 14:19 l2bin_aquarius
cms_optics 3731683 May 21 14:19 l2gen_aquarius
cms_optics 123608 May 21 14:19 landbin
cms_optics 23032 May 21 14:19 landtimebin
cms_optics 512696 May 21 14:19 mk_aquarius_ancillary_data
cms_optics 9152 May 21 14:19 oisst_info
cms_optics 14030 May 21 14:19 solar_xray
cms_optics 13169 May 21 14:19 swh
cms_optics 13682 May 21 14:19 tec
cms_optics 13000 May 21 14:19 time_offset
cms_optics 96916 May 21 14:56 l0fix_modis
cms_optics 101714 May 21 14:56 l0cnst_write_modis
cms_optics 102355 May 21 14:56 l0chunk_modis
cms_optics 13933 May 21 14:56 pdsmerge
cms_optics 13958 May 21 14:56 pdsinfo
cms_optics 31600 May 21 14:56 l1aextract_modis
cms_optics 10171 May 21 14:56 geocheck_modis
cms_optics 121374 May 21 14:56 nccmp
cms_optics 2212508 May 21 14:56 l1bgen_modist
cms_optics 2210569 May 21 14:56 l1bgen_modisa
cms_optics 92602 May 21 14:56 atteph_info_modis
cms_optics 2720679 May 21 14:57 geogen_modis
cms_optics 77853 May 21 14:57 l1bextract_meris
cms_optics 41209 May 21 14:57 l1asubset_modis
cms_optics 925261 May 21 14:57 geolocate_viirs
cms_optics 936820 May 21 14:57 calibrate_viirs
cms_optics 133042 May 21 14:57 val_extract
cms_optics 134776 May 21 14:57 sstval_extract
cms_optics 1854756 May 21 14:57 l1agen_modis
cms_optics 231956 May 21 14:57 l2brsgen
cms_optics 52475 May 21 14:57 l1aextract_seawifs
cms_optics 110515 May 21 14:57 get_product_info
cms_optics 234560 May 21 14:57 l2mapgen
cms_optics 126546 May 21 14:57 l2extract
cms_optics 2393572 May 21 14:57 l2bin64
cms_optics 2389538 May 21 14:57 l2bin
cms_optics 310931 May 21 14:57 l3bin64
cms_optics 235783 May 21 14:57 l3rebin_meris64
cms_optics 237215 May 21 14:57 l3rebin_meris
cms_optics 306073 May 21 14:57 l3binmerge64
cms_optics 308828 May 21 14:57 l3binmerge
cms_optics 312427 May 21 14:57 l3bin
cms_optics 452184 May 21 14:57 l2binmatch64
cms_optics 453279 May 21 14:57 l2binmatch
cms_optics 597214 May 21 14:57 l3mapgen
cms_optics 375225 May 21 14:57 l3bindump64
cms_optics 376350 May 21 14:57 l3bindump
cms_optics 596963 May 21 14:57 l3mapgen64
cms_optics 2815728 May 21 14:57 l1info
cms_optics 2841197 May 21 14:58 lonlat2pixline
cms_optics 3231896 May 21 14:58 l1mapgen
cms_optics 3006753 May 21 14:58 l1bgen_generic
cms_optics 3232148 May 21 14:58 l1brsgen
cms_optics 4987669 May 21 14:59 l1det2det
cms_optics 4983649 May 21 14:59 vcalmerge
cms_optics 5070805 May 21 14:59 l3gen
cms_optics 5101189 May 21 14:59 l2gen
cms_optics 5068247 May 21 14:59 l3gen64
Are there a couple of things left out of the VIIRS build? I have issued this command:
./install_ocssw.py -v -c -i ocssw --src --aquarius --avhrr --czcs --goci --hico --meris --aqua --terra --mos --msi --ocm1 --ocm2 --octs --olcis3a --oli --osmi --seawifs --viirsn --viirsj1
On both a clean CentOS6 virtual machine and a clean RHEL6 cluster environment. Followed directions https://seadas.gsfc.nasa.gov/build_ocssw/rhel/
In both cases everything appeared to build correctly.
However, this is what I see in the bin dir:
[oo_processing@optics0 bin]$ ll *viirs*
cms_optics 936820 May 21 14:57 calibrate_viirs
cms_optics 925261 May 21 14:57 geolocate_viirs
cms_optics 155624 May 21 14:19 l1aextract_viirs
cms_optics 7299556 May 21 14:19 l2bin_viirs
cms_optics 728728 May 21 14:19 viirs_obc
NOTE that the two files (calibrate_viirs and geolocate_viirs) were compiled (see time stamps) and work. l2bin_viirs was not compiled, but it seems to work without compiling.
BUT these two files (not built) still error out:
[oo_processing@optics0 bin]$ ./l1aextract_viirs
./l1aextract_viirs: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./l1aextract_viirs)
[oo_processing@optics0 bin]$ ./viirs_obc
./viirs_obc: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by ./viirs_obc)
./viirs_obc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./viirs_obc)
l1aextract_viirs is the first program I use in my VIIRS processing.
In fact, here is the bin dir: 14:19 is when I did the ./install_ocssw.py and anything after 14:56 in BOLD is newly compiled)
[oo_processing@optics0 bin]$ ll -ltr
total 80128
cms_optics 8848 May 21 14:19 fixrgb
cms_optics 155624 May 21 14:19 l1aextract_viirs
cms_optics 14 May 21 14:19 l1bgen -> l1bgen_generic
cms_optics 7299556 May 21 14:19 l2bin_viirs
cms_optics 309648 May 21 14:19 smigen
cms_optics 27928 May 21 14:19 smitoppm
cms_optics 728728 May 21 14:19 viirs_obc
cms_optics 17872 May 21 14:19 bindepths
cms_optics 44848 May 21 14:19 biosmap
cms_optics 71880 May 21 14:19 interp_hycom_ascii
cms_optics 105256 May 21 14:19 l0cnst_read_modis
cms_optics 32336 May 21 14:19 l0info_seawifs
cms_optics 22304 May 21 14:19 l0regen_seawifs
cms_optics 439800 May 21 14:19 l1agen_seawifs
cms_optics 165953 May 21 14:19 l1info_aquarius
cms_optics 854350 May 21 14:19 l2bin_aquarius
cms_optics 3731683 May 21 14:19 l2gen_aquarius
cms_optics 123608 May 21 14:19 landbin
cms_optics 23032 May 21 14:19 landtimebin
cms_optics 512696 May 21 14:19 mk_aquarius_ancillary_data
cms_optics 9152 May 21 14:19 oisst_info
cms_optics 14030 May 21 14:19 solar_xray
cms_optics 13169 May 21 14:19 swh
cms_optics 13682 May 21 14:19 tec
cms_optics 13000 May 21 14:19 time_offset
cms_optics 96916 May 21 14:56 l0fix_modis
cms_optics 101714 May 21 14:56 l0cnst_write_modis
cms_optics 102355 May 21 14:56 l0chunk_modis
cms_optics 13933 May 21 14:56 pdsmerge
cms_optics 13958 May 21 14:56 pdsinfo
cms_optics 31600 May 21 14:56 l1aextract_modis
cms_optics 10171 May 21 14:56 geocheck_modis
cms_optics 121374 May 21 14:56 nccmp
cms_optics 2212508 May 21 14:56 l1bgen_modist
cms_optics 2210569 May 21 14:56 l1bgen_modisa
cms_optics 92602 May 21 14:56 atteph_info_modis
cms_optics 2720679 May 21 14:57 geogen_modis
cms_optics 77853 May 21 14:57 l1bextract_meris
cms_optics 41209 May 21 14:57 l1asubset_modis
cms_optics 925261 May 21 14:57 geolocate_viirs
cms_optics 936820 May 21 14:57 calibrate_viirs
cms_optics 133042 May 21 14:57 val_extract
cms_optics 134776 May 21 14:57 sstval_extract
cms_optics 1854756 May 21 14:57 l1agen_modis
cms_optics 231956 May 21 14:57 l2brsgen
cms_optics 52475 May 21 14:57 l1aextract_seawifs
cms_optics 110515 May 21 14:57 get_product_info
cms_optics 234560 May 21 14:57 l2mapgen
cms_optics 126546 May 21 14:57 l2extract
cms_optics 2393572 May 21 14:57 l2bin64
cms_optics 2389538 May 21 14:57 l2bin
cms_optics 310931 May 21 14:57 l3bin64
cms_optics 235783 May 21 14:57 l3rebin_meris64
cms_optics 237215 May 21 14:57 l3rebin_meris
cms_optics 306073 May 21 14:57 l3binmerge64
cms_optics 308828 May 21 14:57 l3binmerge
cms_optics 312427 May 21 14:57 l3bin
cms_optics 452184 May 21 14:57 l2binmatch64
cms_optics 453279 May 21 14:57 l2binmatch
cms_optics 597214 May 21 14:57 l3mapgen
cms_optics 375225 May 21 14:57 l3bindump64
cms_optics 376350 May 21 14:57 l3bindump
cms_optics 596963 May 21 14:57 l3mapgen64
cms_optics 2815728 May 21 14:57 l1info
cms_optics 2841197 May 21 14:58 lonlat2pixline
cms_optics 3231896 May 21 14:58 l1mapgen
cms_optics 3006753 May 21 14:58 l1bgen_generic
cms_optics 3232148 May 21 14:58 l1brsgen
cms_optics 4987669 May 21 14:59 l1det2det
cms_optics 4983649 May 21 14:59 vcalmerge
cms_optics 5070805 May 21 14:59 l3gen
cms_optics 5101189 May 21 14:59 l2gen
cms_optics 5068247 May 21 14:59 l3gen64
Yea, the lawyers got in the way of l1aextract_viirs. I'm working on a way put the IP (intellectual property) suspect code into a lib since we cannot release the source. I'll get back to you on that one in a bit.
I think l2bin_viirs used to bin the SDR files from NOAA. I'll remember to delete that one from everywhere.
don
I think l2bin_viirs used to bin the SDR files from NOAA. I'll remember to delete that one from everywhere.
don
We have updated the binaries to work on CentOS 6 (and newer distros). You should no longer have to compile to get things to work.
Let me know if you have any issues with the new binaries.
don
Let me know if you have any issues with the new binaries.
don
Don,
I have tested the binaries on CentOS6.9 and CentOS7.5, and on the RHEL 6.8 cluster environment. I have not run into any issues so far.
THANKS SO MUCH
Brock
I have tested the binaries on CentOS6.9 and CentOS7.5, and on the RHEL 6.8 cluster environment. I have not run into any issues so far.
THANKS SO MUCH
Brock
Thanks. Building on a CentOS 6 machine for binary distribution seems to work for most flavors of linux.
I'm working on compiling instructions now.
don
I'm working on compiling instructions now.
don
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