[slurm-users] blastx fails with "Error memory mapping"

[Mahmood Naderan]

Hi,
Although I can run the blastx command on terminal on all nodes, I can not
use slurm for that due to a so called "memory map error".
Please see below that I pressed ^C after some seconds when running via
terminal.

Fri Jan 24 15:29:57 +0330 2020
[shams@hpc ~]$ blastx -db ~/ncbi-blast-2.9.0+/bin/nr -query
~/khTrinityfilterless1.fasta -max_target_seqs 5 -outfmt 6 -evalue 1e-5
-num_threads 2
^C
[shams@hpc ~]$ date
Fri Jan 24 15:30:09 +0330 2020


However, the following script fails

[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:$PATH
blastx -db ~/ncbi-blast-2.9.0+/bin/nr -query ~/khTrinityfilterless1.fasta
-max_target_seqs 5 -outfmt 6 -evalue 1e-5 -num_threads 2
[shams@hpc ~]$ sbatch slurm_blast.sh
Submitted batch job 284
[shams@hpc ~]$ cat my_blast.log
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=0x7f9a0fb3e505
      blastx ???:0 blastx() [0x9ca345] offset=0x0 addr=0x9ca345



Any idea about that?


Regards,
Mahmood