Hi Mahmood, You may check here and see if it helps you: https://unix.stackexchange.com/questions/345595/how-to-set-ulimits-on-service-with-systemd
On Mon, Jan 27, 2020 at 2:41 PM Mahmood Naderan <mahmood...@gmail.com> wrote: > 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 > > > > >
