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Hello, I have mpiBLAST 1.4.0 installed on a 128 node cluster with
SGE. While mpiBLAST worked fine for a while, all of a sudden I started getting errors
with no apparent cause. I used the same submission script and the same
parameters except that I increased number of processors from 2 to 16 (later
when I dropped the number of CPUs, I kept getting the following output in the […].o<PID>
file): cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.phr
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.phr source = /ibrixfs1/users/mpiblast/yeast.nt.000.phr dest =
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.phr ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.pin
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pin source = /ibrixfs1/users/mpiblast/yeast.nt.000.pin dest =
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pin ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.psq
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psq source = /ibrixfs1/users/mpiblast/yeast.nt.000.psq dest =
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psq ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.pnd
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pnd source = /ibrixfs1/users/mpiblast/yeast.nt.000.pnd dest =
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pnd ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.pni
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pni source = /ibrixfs1/users/mpiblast/yeast.nt.000.pni dest =
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.pni ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.psd
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psd source = /ibrixfs1/users/mpiblast/yeast.nt.000.psd dest = /ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psd ret_value = 32512 cp command failed! command: cp /ibrixfs1/users/mpiblast/yeast.nt.000.psi
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psi source = /ibrixfs1/users/mpiblast/yeast.nt.000.psi dest = /ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nt.000.psi ret_value = 32512 [9] 22870 (9) unable to
copy fragment! [9] [MPI Abort by user] Aborting Program! Could not remove
/ibrixfs1/users/mpiblast/runs/mpiblast_tempZyrpla/yeast.nth8EHTO.pal:: No such
file or directory Terminating processes.. done. I tried changing ‘dest’ directory in the ncbirc
file from /tmp to the network drive to try to avoid copying of the file but it
did not help. I also tried deleting all file in the /tmp directory across all
the nodes but that did not help either. Any suggestions or insight would be greatly appreciated, Enis |
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