Since BGL does not have local disk in the compute node, I usually set
TMPDIR( or MPE_TMPDIR ) to $PWD where you program resides. If you are
using cqsub, here is the command:
cqsub -e MPE_TMPDIR=${PWD} -n <num_of_nodes> -t <TIME> -C $PWD dock5
I used /pvfs before, but it was performing worse than $PWD. i.e. you will
see the internal state, CLOG_Buffer_write2disk, is even longer. The mpe2
README file, ~chan/mpe_work/mpe2/README, contains description of the
environmental variables that MPE reads. You may want to take a look.
A.Chan
On Sun, 16 Oct 2005, Kaitlyn Hwang wrote:
I am testing the scalabilty of Dock5 with 100,000 ligands on bgl.
With 1000 ligands, Dock5 with logging enabled works fine.
However with 100,000 ligands I get the following error.
<Oct 14 15:53:36> BE_MPI (Info) : IO - Threads initialized
/home/chan/mpe_work/mpe2/src/logging/src/clog_buffer.c:CLOG_Buffer_localIO_init4write()
-
Fail to open the temporary logfile /tmp/clog2_taskID=0000_WvwFhk.
Check if the directory where the logfile resides exists
and the corresponding file system is NOT full.
If not so, set environmental variable TMPDIR to a bigger filesystem.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0<Oct 14
20:52:07> BE_MPI (Info) : IO - Listening thread terminated
What is a better location to set the TMPDIR?
kaitlyn
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