GLIBC problem is back... [CentOS 7 RIP]

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treble
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GLIBC problem is back... [CentOS 7 RIP]

by treble » Tue Jan 09, 2024 7:17 pm America/New_York

Using SeaDAS 8.4.1 with the latest tag (V2023.3) gives me the GLIBC error again on CentOS 7. See this old discussion: viewtopic.php?t=1419

V2023.2 still works fine...:

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[/opt/seadas/seadas_8.4.1/ocssw 1016]$ install_ocssw --installed_tag

WARNING: --tag is required to get the proper bundle list.

installedTag = V2023.2
[/opt/seadas/seadas_8.4.1/ocssw 1017]$ l2gen -version
msl12 9.6.0-V2023.1 (Apr  4 2023 11:30:59)
This is the output with V2023.3:

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[/opt/seadas/seadas_8.4.1/ocssw 1024]$ install_ocssw --installed_tag

WARNING: --tag is required to get the proper bundle list.

installedTag = V2023.3
[/opt/seadas/seadas_8.4.1/ocssw 1025]$ l2gen -version
l2gen: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by l2gen)
l2gen: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by l2gen)
l2gen: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by l2gen)
l2gen: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by l2gen)
l2gen: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data1/opt/seadas/seadas_8.4.1/ocssw/bin/../lib/libbin.so)
l2gen: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /data1/opt/seadas/seadas_8.4.1/ocssw/bin/../lib/libbin.so)
...
I tried to compile from source code but was not successful...
Last edited by treble on Fri Jan 12, 2024 12:59 pm America/New_York, edited 1 time in total.

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OB.DAAC - SeanBailey
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Re: GLIBC problem is back...

by OB.DAAC - SeanBailey » Thu Jan 11, 2024 9:07 am America/New_York

CentOS7 is end of life in June. We no longer have (or are allowed to have) a CentOS7 machine, the "oldest" we have is RHEL8 (which is what V2023.3 was compiled on). Since it still works for you, you can continue to use V2023.2 or look to upgrade your server to an OS with a longer support cycle.

Sean

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Re: GLIBC problem is back...

by treble » Fri Jan 12, 2024 12:45 pm America/New_York

Ah, that is unfortunate. Especially since the high performance computer cluster at our university is running CentOS 7 as well...

I will have to build from source in the future then I am afraid. I tried it now as well (following the directions for CentOS on the website) but it failed at compiling hdf4 with a not so descriptive error:

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Working on hdf4
Extracting hdf-4.2.16.tar.gz
patching file hdf/src/hlimits.h
Unknown error encountered installing hdf4

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Re: GLIBC problem is back... [CentOS 7 RIP]

by OB.DAAC - SeanBailey » Sat Jan 13, 2024 9:44 am America/New_York

CentOS7 had a good run.

The error message you saw was from the wrapper "BuildIt.py" script. You can build the hdf4 by itself and see what the actually complaint (navigate to opt/src/hdf4 and run it's BuildIt script). It is likely resolvable (but without access to a CentOS7 machine, I'm afraid we can't be of much help here...)

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Re: GLIBC problem is back... [CentOS 7 RIP]

by treble » Tue Jan 16, 2024 4:26 pm America/New_York

Thanks, it fails on linking the jpeg libraries. See last pertinent part where it fails below. Earlier on I see that it doesn't use the compiled jpeg libraries but the system ones... Not sure how to tell cmake or whatever to use the one in the SeaDAS directory (it is located in $OCSSWROOT/opt/lib/libjpeg.so, I don't see libz.so in $OCSSWROOT):

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-- ....All Warnings are enabled
-- Could NOT find JPEG (missing: JPEG_DIR)
-- Found JPEG: /share/software/user/open/java/1.8.0_131/jre/lib/amd64/libjpeg.so (found version "90") 
-- JPEGLIB is ON
-- Could NOT find ZLIB (missing: ZLIB_DIR)
-- Found ZLIB: /share/software/user/open/zlib/1.2.11/lib/libz.so (found version "1.2.11") 
Here is the error and what leads up to it:

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[ 34%] Building C object hdf/test/CMakeFiles/testhdf.dir/tvset.c.o
[ 34%] Building C object hdf/test/CMakeFiles/testhdf.dir/tvsfpack.c.o
[ 34%] Building C object hdf/test/CMakeFiles/testhdf.dir/vers.c.o
[ 34%] Linking C executable ../../bin/testhdf
CMakeFiles/testhdf.dir/tusejpegfuncs.c.o: In function `comp_using_jpeglib':
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:66: undefined reference to `jpeg_std_error'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:69: undefined reference to `jpeg_CreateCompress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:84: undefined reference to `jpeg_stdio_dest'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:99: undefined reference to `jpeg_set_defaults'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:102: undefined reference to `jpeg_set_quality'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:108: undefined reference to `jpeg_start_compress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:119: undefined reference to `jpeg_write_scanlines'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:123: undefined reference to `jpeg_finish_compress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:133: undefined reference to `jpeg_destroy_compress'
CMakeFiles/testhdf.dir/tusejpegfuncs.c.o: In function `decomp_using_jpeglib':
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:185: undefined reference to `jpeg_std_error'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:188: undefined reference to `jpeg_CreateDecompress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:191: undefined reference to `jpeg_stdio_src'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:194: undefined reference to `jpeg_read_header'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:202: undefined reference to `jpeg_start_decompress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:217: undefined reference to `jpeg_read_scanlines'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:229: undefined reference to `jpeg_finish_decompress'
/home/groups/user/seadas/ocssw/opt/src/hdf4/hdf-4.2.16/hdf/test/tusejpegfuncs.c:232: undefined reference to `jpeg_destroy_decompress'
../../bin/libhdf.so.4.17.2: undefined reference to `jpeg_resync_to_restart'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/testhdf] Error 1
make[1]: *** [hdf/test/CMakeFiles/testhdf.dir/all] Error 2
make: *** [all] Error 2
Unknown error encountered installing hdf4
It's not super urgent, but it would be nice if I got it to compile.

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