Comments (11)
pescobar
commented on July 20, 2024
CCing those who contributed to this easyblock in case they can give any feedback @AndiH @jfgrimm @appolloford @boegel
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jfgrimm
commented on July 20, 2024
hmm, don't think I've seen that issue before. I'll have a go at building on ubuntu 22.04
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jfgrimm
commented on July 20, 2024
I can't reproduce this on any of my Ubuntu 22.04 systems
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cgross95
commented on July 20, 2024
We see this exact same issue on Ubuntu 22.04 building NVHPC-23.7-CUDA-12.1.1.eb. We haven't tried the workaround yet. We can also provide any other information from our configuration if it would be helpful for reproducing.
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cgross95
commented on July 20, 2024
Here is a test report.
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AndiH
commented on July 20, 2024
I'm really no EB expert, just one of the authors of the EasyBlock.
To me, it sounds like the compiler doesn't look in the right directories for the library objects; i.e. the LD_LIBRARY_PATH may be incomplete. Not sure, though, if this falls into EasyBuild's responsibility…
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pescobar
commented on July 20, 2024
@jfgrimm can you try this to check what libraries you link?
$> module purge
$> module load NVHPC/23.7-CUDA-12.3.0
$> cat <<EOF > minimal.cpp
#include <ranges>
int main(){ return 0; }
EOF
$> nvc++ minimal.cpp -o minimal
$> ldd minimal
This is what I get in my system. The only difference is that I had to compile the binary using nvc++ -L/lib/x86_64-linux-gnu minimal.cpp -o minimal
$> ldd minimal
linux-vdso.so.1 (0x00007ffdf57f9000)
libatomic.so.1 => /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libatomic.so.1 (0x00007f1ff6e24000)
libnvhpcatm.so => /scicore/soft/easybuild/apps/NVHPC/23.7-CUDA-12.3.0/Linux_x86_64/23.7/compilers/lib/libnvhpcatm.so (0x00007f1ff6c00000)
libstdc++.so.6 => /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libstdc++.so.6 (0x00007f1ff69d8000)
libnvomp.so => /scicore/soft/easybuild/apps/NVHPC/23.7-CUDA-12.3.0/Linux_x86_64/23.7/compilers/lib/libnvomp.so (0x00007f1ff5800000)
libnvcpumath.so => /scicore/soft/easybuild/apps/NVHPC/23.7-CUDA-12.3.0/Linux_x86_64/23.7/compilers/lib/libnvcpumath.so (0x00007f1ff5200000)
libnvc.so => /scicore/soft/easybuild/apps/NVHPC/23.7-CUDA-12.3.0/Linux_x86_64/23.7/compilers/lib/libnvc.so (0x00007f1ff4e00000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1ff4bd8000)
libgcc_s.so.1 => /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libgcc_s.so.1 (0x00007f1ff69b7000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1ff68d0000)
/lib64/ld-linux-x86-64.so.2 (0x00007f1ff6e30000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1ff68cb000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1ff68c6000)
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jfgrimm
commented on July 20, 2024
oh, I just realised that although I installed EB 4.9.1, I was still building with 4.9.0...
I now get the same error 🤦
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jfgrimm
commented on July 20, 2024
I'm guessing that the issue is with the generated localrc. I don't think this is actually on easybuild doing something weird, I get the same issue if I manually run makelocalrc -x -gcc $(which gcc) -gpp $(which g++) -g77 $(which gfortran)
Adding the following line to the generated localrc fixes the issue for me:
set DEFLIBDIR=/lib/x86_64-linux-gnu;
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pescobar
commented on July 20, 2024
I noticed this line which is specific to debian systems
but it's not applied for versions < 21 . See here
patching the easyblock like this also workarounds the issue but to be honest I am not sure what would be the right fix
diff -ru /scicore/soft/easybuild/apps/EasyBuild/4.9.1/lib/python3.10/site-packages/easybuild/easyblocks/n/nvhpc.py ~/tmp/nvhpc.py
--- /scicore/soft/easybuild/apps/EasyBuild/4.9.1/lib/python3.10/site-packages/easybuild/easyblocks/n/nvhpc.py 2024-04-17 11:23:00.892718404 +0200
+++ /scicore/home/scicore/easybuild/tmp/nvhpc.py 2024-04-17 12:51:54.115386938 +0200
@@ -54,9 +54,6 @@
# contents for siterc file to make PGI/NVHPC pick up $LIBRARY_PATH
# cfr. https://www.pgroup.com/support/link.htm#lib_path_ldflags
SITERC_LIBRARY_PATH = """
-# get the value of the environment variable LIBRARY_PATH
-variable LIBRARY_PATH is environment(LIBRARY_PATH);
-
# split this value at colons, separate by -L, prepend 1st one by -L
variable library_path is
default($if($LIBRARY_PATH,-L$replace($LIBRARY_PATH,":", -L)));
@@ -188,12 +185,11 @@
if os.path.islink(path):
os.remove(path)
- if LooseVersion(self.version) < LooseVersion('21.3'):
- # install (or update) siterc file to make NVHPC consider $LIBRARY_PATH
- siterc_path = os.path.join(compilers_subdir, 'bin', 'siterc')
- write_file(siterc_path, SITERC_LIBRARY_PATH, append=True)
- self.log.info("Appended instructions to pick up $LIBRARY_PATH to siterc file at %s: %s",
- siterc_path, SITERC_LIBRARY_PATH)
+ # install (or update) siterc file to make NVHPC consider $LIBRARY_PATH
+ siterc_path = os.path.join(compilers_subdir, 'bin', 'siterc')
+ write_file(siterc_path, SITERC_LIBRARY_PATH, append=True)
+ self.log.info("Appended instructions to pick up $LIBRARY_PATH to siterc file at %s: %s",
+ siterc_path, SITERC_LIBRARY_PATH)
# The cuda nvvp tar file has broken permissions
adjust_permissions(self.installdir, stat.S_IWUSR, add=True, onlydirs=True)
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pescobar
commented on July 20, 2024
To summarize, the problem is that debian systems need to have folder /usr/lib/x86_64-linux-gnu/ in env var LIBRARY_PATH. This is needed to compile the example in the sanity_check step and also to build any other easyconfig using the nvhpc toolchain
possible solutions are:
-
update the easyblock so that the generated rc file fixes it
-
update the easyblock to use the right LIBRARY_PATH for sanity_check step and define the required env vars in the nvhpc easyconfig .e.g add this to the easyconfigs
allow_append_abs_path = True
modextrapaths = {
'LD_LIBRARY_PATH': 'Linux_%(arch)s/%(version)s/compilers/extras/qd/lib/',
'LIBRARY_PATH': 'Linux_%(arch)s/%(version)s/compilers/extras/qd/lib/'
}
modextrapaths_append = {
'LD_LIBRARY_PATH': '/usr/lib/x86_64-linux-gnu',
'LIBRARY_PATH': '/usr/lib/x86_64-linux-gnu'
}
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