From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Jan 16 2019 - 12:30:48 CST
I got my system to run over several nodes now using Slurm, but it terminates now with the ERROR:
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Error on renaming file md1Solv_New3PTBP.xst to md1Solv_New3PTBP.xst.BAK: No such file or directory
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to open text file md1Solv_New3PTBP.xst: File exists
I am assuming it has something to do with running on several nodes and the file is attempting to be rewritten when on other nodes and it does not want to do this...The dcd file will also pose a problem right...? I need NAMD to overwrite the output files..?
Below is my "Slurm Input" script...
#SBATCH --job-name=Seibold # Job name
#SBATCH --partition=mridata # Partition Name (Required)
##SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
##SBATCH --mail-user=stevesi_at_ku.edu # Where to send mail
#SBATCH --output=md1_3PTBP_%j.log # Standard output and error log
pwd; hostname; date
#module load namd/2.12_multicore
echo "Running on $SLURM_CPUS_ON_NODE cores"
mpirun ~/NAMD2/NAMD_2.13_Linux-x86_64/namd2 md1_3PTBP.namd
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