[gmx-users] re: implicit solvent and REMD

[Ilya Chorny]

Hello 

I've been trying to test the REMD code but have been having some
problems.

I set up 4 remdrun(0-4).tpr files.

I gave the following command.

"~ichorny/bin/mpirun n7-8 -np 4 -wd $PWD mdrun_remd -np 4 -deffnm
remdrun -v -redt 500 -ren 4 -relog -repe -multi > & outlog"

It seems to startup just fine but then quits. I test the starting
structure at on temperature with the same mdp file and it run fine.
Below is the output from the outlog file. Everything looks ok but it
just decides to die.

Thanks

Ilya

Back Off! I just backed up remdrun1.log to ./#remdrun1.log.1#

Back Off! I just backed up remdrun2.log to ./#remdrun2.log.1#

Back Off! I just backed up remdrun3.log to ./#remdrun3.log.1#

Back Off! I just backed up remdrun0.log to ./#remdrun0.log.1#
Reading file remdrun3.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun1.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun3.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun1.tpr, VERSION 3.1.4 (single precision)
Getting Loaded...
Reading file remdrun2.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun0.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun2.tpr, VERSION 3.1.4 (single precision)
Reading file remdrun0.tpr, VERSION 3.1.4 (single precision)
Loaded with Gravy

Opening temperature logfile

Back Off! I just backed up remdrun2.edr to ./#remdrun2.edr.1#

Back Off! I just backed up remdrun1.edr to ./#remdrun1.edr.1#

Back Off! I just backed up remd_T.xvg to ./#remd_T.xvg.1#
Opening potential energy logfile
starting mdrun 'Protein in water'
500000 steps,   1000.0 ps.

starting mdrun 'Protein in water'
500000 steps,   1000.0 ps.


Back Off! I just backed up remdrun3.edr to ./#remdrun3.edr.1#

Back Off! I just backed up pe.xvg to ./#pe.xvg.1#
------------------------------------------------------------------------
-----
starting mdrun 'Protein in water'
500000 steps,   1000.0 ps.

One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return 
0" or "exit(0)" in your C code before exiting the application.
   
PID 26251 failed on node n7 (192.168.0.7)Got info from self:
IDTlist[0].ID = 0  - IDTlist[0].T = 275.0
Got info from node 1: IDTlist[1].ID = 1  - IDTlist[1].T = 300.0
Got info from node 2: IDTlist[2].ID = 2  - IDTlist[2].T = 325.0
 due to signal 11.
------------------------------------------------------------------------
-----
Got info from node 3: IDTlist[3].ID = 3  - IDTlist[3].T = 350.0
Number of unique temperatures: 4
Making a pair: 0 1
Making a pair: 0 2
Making a pair: 0 3
Making a pair: 1 2
Making a pair: 1 3
Making a pair: 2 3
NNODES: 4
reTEMP:  4
Temperature found:  275.0
Temperature found:  300.0
Temperature found:  325.0
Temperature found:  350.0
testtemps thinks that 275 and 300 are neighbors.
testtemps thinks that 300 and 325 are neighbors.
testtemps thinks that 325 and 350 are neighbors.
Number of possible exchanges (reNUMPAIRS): 3
nonunique pair 0: 0 - 1
nonunique pair 1: 0 - 2
nonunique pair 2: 0 - 3
nonunique pair 3: 1 - 2
nonunique pair 4: 1 - 3
nonunique pair 5: 2 - 3
unique pair 0: 0 - 1
unique pair 1: 1 - 2
unique pair 2: 2 - 3
Hey, you made it into do_md anyway...