[ERROR] libmpi_mpifh.so: undefined reference to `memcpy@GLIBC_2.14' #70
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Hi, can you provide your important settings and a complete log for your build process? |
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important settings |
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Did you compile TDEP successfully before? Do the other binaries compile (when commenting out |
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for dump_dynamical_matrices, i can successfully compile for other TDEP release. I obtain the newest TDEP release by git clone, and then Compiling failed by the same conda method. |
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Hello, I think this has nothing to do with TDEP. Your anaconda environment is inconsistent /home/cqwl222/anaconda3/envs/tdep/lib/./libpmix.so.2: undefined reference to clock_gettime@GLIBC_2.17' These 2 libs have been installed with different glibc versions, so it's normal they don't link together properly. Try to re-install your conda stack. It could be that the older releases did not use clock_gettime or memcpy in the same way, or something like that. |
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NB: it fails in dump_xxx because it's the first executable built. I suspect the others will do the same |
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I find TDEP release 24.01 could be successfully installed through conda environment. However, for the same conda environment, the newest TDEP by git clone fails. |
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@Guodonglin-cqust what happens if you commment out |
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If i commment out dump_dynamical_matrices in build_things.sh, the newest TDEP by git clone could be successfully installed through conda environment. |
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@Guodonglin-cqust can you share your log output for the rest of the compilation when |
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@Guodonglin-cqust can you check if #76 fixes the problem? |
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I download the code from branch (https://github.com/tdep-developers/tdep/tree/70-error-libmpi_mpifhso-undefined-reference-to-memcpyglibc_214) |
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Can you run Edit: run this in the folder |
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You are on the wrong branch, which is equivalent to the |
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Still wrong branch I think. What does |
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Please familiarize with git to the extent that you can use the branch in the pull request. |
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@Guodonglin-cqust for the record, the command should be If that does not work, try ssh instead of https |
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1.git clone https://github.com/flokno/tdep.git 2.git checkout 70-error-libmpi_mpifhso-undefined-reference-to-memcpyglibc_214 branch '70-error-libmpi_mpifhso-undefined-reference-to-memcpyglibc_214' set up to track 'origin/70-error-libmpi_mpifhso-undefined-reference-to-memcpyglibc_214'. 3../build_things.sh --nthreads_make 4 4.Printing bashrc_tdep, append these lines to your .bashrc for stuff to work nicely Everything should be set up and good to go! Thank you for your patient guidance. |
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Good, I will merge the branch then to |
flokno
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Jul 10, 2024
* fix | linking for dump_dynamical_matrices * fix compilation | remove superfluous LIBS - closes #70
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I use the conda to install the tdep code, which is obtained by git clone https://github.com/tdep-developers/tdep.git. However, i meet these following errors
Building dump_dynamical_matrices
/home/cqwl222/anaconda3/envs/tdep/bin/../lib/gcc/x86_64-conda-linux-gnu/11.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: //home/cqwl222/anaconda3/envs/tdep/lib/./libpmix.so.2: undefined reference to
clock_gettime@GLIBC_2.17' /home/cqwl222/anaconda3/envs/tdep/bin/../lib/gcc/x86_64-conda-linux-gnu/11.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: //home/cqwl222/anaconda3/envs/tdep/lib/libmpi_mpifh.so: undefined reference tomemcpy@GLIBC_2.14'collect2: error: ld returned 1 exit status
make: *** [Makefile:24: ../../build/dump_dynamical_matrices/dump_dynamical_matrices] Error 1
How to resolve this problem.
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