Reply To: Rosetta3.2.1-LAM-MPI Run-Problem-More than 2 processor Jobs

[Anonymous]

Hi Steven:

I have applied the patch that you had sent me

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PATCH

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[ravi@torkv rosetta_source]$ ./scons.py bin mode=release extras=mpi
scons: Reading SConscript files …
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbInitio_MPI.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/AbInitio_MPI.cc
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/AbInitio_MPI.linuxgccrelease -Wl,-rpath=/opt/nasapps/build/Rosetta/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/mpi build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbInitio_MPI.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/64/x86/gcc/mpi -Lsrc -L/usr/local/lib -L/usr/lib -L/lib -L/lib64 -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: “build/src/release/linux/2.6/64/x86/gcc/mpi/AbInitio_MPI.linuxgccrelease” as “bin/AbInitio_MPI.linuxgccrelease”
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/AbInitio_MPI.mpi.linuxgccrelease -Wl,-rpath=/opt/nasapps/build/Rosetta/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/mpi build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbInitio_MPI.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/64/x86/gcc/mpi -Lsrc -L/usr/local/lib -L/usr/lib -L/lib -L/lib64 -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: “build/src/release/linux/2.6/64/x86/gcc/mpi/AbInitio_MPI.mpi.linuxgccrelease” as “bin/AbInitio_MPI.mpi.linuxgccrelease”
scons: done building targets.

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MPIRUN with NP 2 WORKS FINE

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mpirun -np 2 $rosetta_home/bin/AbinitioRelax.mpi.linuxgccrelease @flags

……
……
……
Total weighted score: 24.862

===================================================================
Finished Abinitio

protocols.abinitio.AbrelaxApplication: (1) Finished _0001 in 7 seconds.
protocols::checkpoint: (1) Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: (1) Deleting checkpoints of Abrelax
protocols.jobdist.JobDistributors: (1) Node: 1 next_job()
protocols.jobdist.JobDistributors: (1) Slave Node 1 — requesting job from master node; tag_ 1
protocols.jobdist.JobDistributors: (0) Master Node –available job? 0
protocols.jobdist.JobDistributors: (0) Master Node — Spinning down node 1
protocols.jobdist.JobDistributors: (0) Node 0 — ready to call mpi finalize
protocols.jobdist.JobDistributors: (1) Node 1 — ready to call mpi finalize
protocols::checkpoint: (0) Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: (0) Deleting checkpoints of Abrelax
protocols::checkpoint: (1) Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: (1) Deleting checkpoints of Abrelax

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–MPIRUN with NP >2 FAILS

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===================================================================
Stage 2
Folding with score1 for 2000

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One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a “return
0″ or “exit(0)” in your C code before exiting the application.

PID 7798 failed on node n0 (129.43.63.50) due to signal 11.

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Could LAM-7.1.4 be an issue?

Thanks

Ravi