AMBER Archive (2009)

Subject: [AMBER] Error message for tutorial 1 (run in parallel)

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon May 04 2009 - 04:05:17 CDT

Dear Sir/Madam,

 

I encountered a parallel run error message when I tried to run the explicit solvent calculations in tutorial 1 with our supercomputer. What does this error message stands for?

 

I am using AMBER8. Our supercomputer consists of 24 nodes. Each node contains two 64-bit Intel quad-core Xeon processors of 3GHz and 8GB of RAM. Each processor consists of 12MB of cache.

The supercomputer uses the Scientific Linux 5.2 as its operating system. Is the system compatible for parallel runs?

 

============================================================================================

[supercomputer]$ mpirun -np 2 /share1/amber8/exe/sander -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst &
[1] 19207
[supercomputer]$
  Unit 9 Error on OPEN: polyAT_wat_min2.rst
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_19304: p4_error: : 1
p0_19304: (0.199219) net_send: could not write to fd=4, errno = 32
rm_l_1_19386: (0.011719) net_send: could not write to fd=5, errno = 32
p1_19308: (2.011719) net_send: could not write to fd=5, errno = 32
============================================================================================

 

Interestingly, when I do the calculations with the following command, the job finished without error message using the same input files.

 

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

[supercomputer]$ mpirun -np 2 /share1/amber8/exe/sander -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst &

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 

Did I do anything wrong here?

 

Best regards and many thanks,

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