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Cannot work in parallel with mpi
#38057 08/21/20 02:12 AM
Joined: Aug 2020
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protein Offline OP
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Hi,
I have installed charmm c45b1 with cmake successfully, but when running with mpirun, it prints the same result for mutiple times. I have also tried with srun, but it won't work in parallel either. Details are as below.

Run with: mpirun -n 4 /gpfs/user/tanyuhao/software/charmm_c45b1/bin/charmm -i ./sexampleout/energy_mutabinds_lb38p.inp path=./sexampleout protname=mutabinds > ./sexampleout/energy.test.out
Input and output are attached as energy_mutabinds_lb38p.txt and energe.test.txt
I am not familiar with the script, but it seems that PRNLEV or WRNLEV are not in it.

I have checked the version of compiler, and assume that charmm and mpi are compiled with the same compiler. Details are as below.
ldd /gpfs/user/tanyuhao/software/charmm_c45b1/bin/charmm
linux-vdso.so.1 => (0x00007ffc85f3e000)
/preload (0x00007ff520d92000)
libmpifort.so.12 => /opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/libmpifort.so.12 (0x00007ff5209e9000)
libmpi.so.12 => /opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/libmpi.so.12 (0x00007ff51fd64000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ff51fb60000)
librt.so.1 => /lib64/librt.so.1 (0x00007ff51f958000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff51f73c000)
libmkl_gf_lp64.so => /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so (0x00007ff51ec56000)
libmkl_sequential.so => /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_sequential.so (0x00007ff51d948000)
libmkl_core.so => /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00007ff51b7b5000)
libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007ff51b493000)
libm.so.6 => /lib64/libm.so.6 (0x00007ff51b191000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007ff51ae89000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007ff51ac63000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff51aa4d000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007ff51a811000)
libc.so.6 => /lib64/libc.so.6 (0x00007ff51a444000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff520f95000)
ldd /opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin/mpiexec
linux-vdso.so.1 => (0x00007ffc95fe2000)
/preload (0x00007f31935af000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f31933ab000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f319318f000)
libm.so.6 => /lib64/libm.so.6 (0x00007f3192e8d000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f3192c77000)
libc.so.6 => /lib64/libc.so.6 (0x00007f31928aa000)
/lib64/ld-linux-x86-64.so.2 (0x00007f31937b2000)

How can I fix the issue?

Thank you in advance!

Attached Files
energy_mutabinds_lb38p.txt (493 Bytes, 41 downloads)
SHA1: 6df28a95251d774d1764fa6124472e0d0b527def
energy.test.txt (52.77 KB, 46 downloads)
SHA1: b5185546bb571aa94ba16295155809d6a6dd681e
Re: Cannot work in parallel with mpi
protein #38062 08/21/20 12:45 PM
Joined: Sep 2003
Posts: 8,532
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rmv Offline
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When the PRNLEV command is used in parallel, you MUST use the NODE option to restrict the scope; try

PRNLEV 3 NODE 0

instead of PRNLEV 0


Rick Venable
computational chemist

Re: Cannot work in parallel with mpi
protein #38065 08/21/20 09:13 PM
Joined: Sep 2003
Posts: 4,810
Likes: 2
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PBEQ does not run in parallel


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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