Excuse me, I see that "ulimit -a" shows unlimited virtual memory size when
the user runs that on terminal. However, when he puts the command in sbatch
script, the value is limited to about 40GB.
[shams@hpc ~]$ ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 256657
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4096
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
[shams@hpc ~]$ cat slurm_blast.sh
#!/bin/bash
#SBATCH --job-name=blast1
#SBATCH --output=my_blast.log
#SBATCH --partition=SEA
#SBATCH --account=fish
#SBATCH --mem=38GB
#SBATCH --nodelist=hpc
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
export PATH=~/ncbi-blast-2.9.0+/bin:$PATH
ulimit -a | grep virtual
ulimit -v 146800640
ulimit -a | grep virtual
blastx -db ~/ncbi-blast-2.9.0+/bin/nr -query ~/khTrinityfilterless1.fasta
-max_target_seqs 5 -outfmt 6 -evalue 1e-5 -num_threads 2
[shams@hpc ~]$ sbatch slurm_blast.sh
Submitted batch job 304
[shams@hpc ~]$ cat my_blast.log
virtual memory (kbytes, -v) 43830476
/var/spool/slurmd/job00304/slurm_script: line 13: ulimit: virtual memory:
cannot modify limit: Operation not permitted
virtual memory (kbytes, -v) 43830476
Error memory mapping:/home/shams/ncbi-blast-2.9.0+/bin/nr.52.psq
openedFilesCount=151 threadID=0
Error: NCBI C++ Exception:
T0
"/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_560232_130.14.18.6_9008__PrepareRelease_Linux64-Centos_1552331742/c++/compilers/unix/../../src/corelib/ncbiobj.cpp",
line 981: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to
access NULL pointer.
Stack trace:
blastx ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x77
addr=0x1d95da7
blastx ???:0 ncbi::CStackTrace::CStackTrace(std::string const&)
offset=0x25 addr=0x1d98465
blastx ???:0 ncbi::CException::x_GetStackTrace() offset=0xA0
addr=0x1ec7330
blastx ???:0 ncbi::CException::SetSeverity(ncbi::EDiagSev)
offset=0x49 addr=0x1ec2169
blastx ???:0 ncbi::CObject::ThrowNullPointerException() offset=0x2D2
addr=0x1f42582
blastx ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x61C
addr=0xf2929c
blastx ???:0 ncbi::blast::CLocalBlast::Run() offset=0x404
addr=0xed4684
blastx ???:0 CBlastxApp::Run() offset=0xC9C addr=0x9cbf7c
blastx ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppDiagStream,
char const*, int*, bool*) offset=0x8E3 addr=0x1da0e13
blastx ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*,
char const* const*, ncbi::EAppDiagStream, char const*, std::string const&)
offset=0x782 addr=0x1d9f6b2
blastx ???:0 main offset=0x5E5 addr=0x9caa05
/lib64/libc.so.6 ???:0 __libc_start_main offset=0xF5
addr=0x7ff1d519e505
blastx ???:0 blastx() [0x9ca345] offset=0x0 addr=0x9ca345
Moreover, the user can not change the virtual size.
I really wonder how can I tell slurm not to change that parameter!!
Regards,
Mahmood
