We are running I-TASSER in gnuparallel mode on our cluster. We've noticed that if two or more jobs execute on the same node that the first one will complete while the others have the following error messages:
cp: cannot create regular file ‘./solve’: Text file busy
cp: cannot create regular file ‘./temp.pdb’: File exists
cp: cannot create regular file ‘./temp.pdb’: File exists
cp: cannot create regular file ‘./temp.pdb’: File exists
cp: cannot create regular file ‘./temp.pdb’: File exists
I am assuming that all the jobs are attempting to write to the same file, rather than writing to a file they exclusively control.
Here are the job starting parameters:
Your setting for running I-TASSER is:
-pkgdir = /sysapps/cluster/software/I-TASSER/5.1
-libdir = /sysapps/cluster/software/ITLIB
-java_home = /usr
-seqname = seq.fasta
-datadir = /hpcdata/scratch/bastmh/20171122/I-TASSER/run_1212344
-outdir = /hpcdata/scratch/bastmh/20171122/I-TASSER/run_1212344
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 24
-LBS = true
-EC = true
-GO = true
The datadir and outdir both include the job number, so they are unique to each run. What can I do to keep the program from attempting to access files in use by other instances of the same program?