Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files:
"In the log file of the code": There are: 1611 Atoms There are: 1611 VSites Charge group distribution at step 0: 101 147 137 152 Grid: 5 x 3 x 3 cells "in the output file reported by cluster": pwd= /home/ppirzade/GROMACS/mytests/small-box-of-water Got 4 slots. compute-1-34 compute-1-34 compute-2-20 compute-2-20 Starting run at: Mon Jun 8 10:27:52 MDT 2009 p2_22627: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_22748: (301.332031) net_send: could not write to fd=5, errno = 32 p2_22627: (301.332031) net_send: could not write to fd=5, errno = 32 p0_21851: (302.351562) net_recv failed for fd = 6 p0_21851: p4_error: net_recv read, errno = : 104 p0_21851: (306.359375) net_send: could not write to fd=4, errno = 32 Ending run at: Mon Jun 8 10:32:59 MDT 2009 "in the error file reported by cluster": Reading file npttest.tpr, VERSION 4.0.4 (single precision) Making 1D domain decomposition 4 x 1 x 1 Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. Payman
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