[gmx-users] mdrun's mpi version error

Tivadar Orban t.orban at csuohio.edu
Sat Oct 26 19:34:51 CEST 2002


Hi,
I'm want to run a test on a MacOSX cluster and I have got this error as 
an output of mdrun (output.mdrun_md) from the demo script provided:
 >>>>>
Getting Loaded...
Reading file cpeptide_md.tpr, VERSION 3.1.5_pre1 (single precision)
Reading file cpeptide_md.tpr, VERSION 3.1.5_pre1 (single precision)
bm_list_29919: (11.707980) wakeup_slave: unable to interrupt slave 0 
pid 29918
p1_15157:  p4_error: : -1
NODEID=1 argc=11
Fatal error: Could not open md1.log
Error on node 1, will try to stop all the nodes
[1] MPI Abort by user Aborting program !
[1] Aborting program!
     p4_error: latest msg from perror: Permission denied
NODEID=2 argc=11
p3_15165:  p4_error: : -1
NODEID=3 argc=11
Fatal error: Could not open md3.log
Error on node 3, will try to stop all the nodes
[3] MPI Abort by user Aborting program !
[3] Aborting program!
     p4_error: latest msg from perror: Permission denied
rm_l_2_29927: (3.158041) net_send: could not write to fd=6, errno = 9
Broken pipe
Broken pipe
rm_l_2_29927:  p4_error: net_send write: -1
     p4_error: latest msg from perror: Bad file descriptor
 >>>>>

I got this error by executing

lamboot (with the specified hosts)
grompp -f md -c ${MOL}_b4md  -p ${MOL} -o ${MOL}_md -np 4 >& ! 
output.grompp_md
mpirun -np 4 -v mdrun -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v 
-g -np 4 >& ! output.mdrun_md

Can anybody help me with this?

Regards,
Tivadar, Orban




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