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BioPsyk / cleansumstats

Convert GWAS sumstat files into a common format with a common reference for positions, rsids and effect alleles.
https://biopsyk.github.io/metadata/#!/form/cleansumstats
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JVM issue on GDK open #354

Closed pappewaio closed 1 year ago

pappewaio commented 2 years ago

Unclear issue on GDK open, Rerunning seems to solve the problem.

[jesgaaopen@fe-open-01 raw_library]$ cat clean_9.err
Successfully read/validated metadata file '/cleansumstats/input/sumstat_9_new_meta2.txt'
Unhandled exception
Type=Segmentation error vmState=0x00000000
J9Generic_Signal_Number=00000018 Signal_Number=0000000b Error_Value=00000000 Signal_Code=00000001
Handler1=00002B07ACC25970 Handler2=00002B07ACFAC920 InaccessibleAddress=0000000000000706
RDI=00002B07D9403180 RSI=0000000000000706 RAX=0000000000000000 RBX=0000000090000002
RCX=0000000000000006 RDX=00002B07D9102E30 R8=00000000FFFFFFFB R9=0000000000000000
R10=00002B07ABBD9C30 R11=0000000000000000 R12=00002B07B0017580 R13=00002B07D9403180
R14=00002B07ABBE8060 R15=00002B07B0985800
RIP=00002B07ABBD960E GS=0000 FS=0000 RSP=00002B07D9402508
EFlags=0000000000010283 CS=0033 RBP=0000000000000000 ERR=0000000000000004
TRAPNO=000000000000000E OLDMASK=0000000000000000 CR2=0000000000000706
xmm0 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm1 76616a2f74706f2f (f: 1953525504.000000, d: 1.713659e+262)
xmm2 62696c2f706d742f (f: 1886221312.000000, d: 1.171191e+166)
xmm3 646573736572706d (f: 1701998720.000000, d: 4.244384e+175)
xmm4 62696c2f73666572 (f: 1936090496.000000, d: 1.171191e+166)
xmm5 000000000003ff00 (f: 261888.000000, d: 1.293899e-318)
xmm6 00002b07acf7bf20 (f: 2901917440.000000, d: 2.337522e-310)
xmm7 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm8 0000000041400000 (f: 1094713344.000000, d: 5.408603e-315)
xmm9 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm10 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm11 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm12 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm13 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm14 0000000000000000 (f: 0.000000, d: 0.000000e+00)
xmm15 0000000000000000 (f: 0.000000, d: 0.000000e+00)
Module=/lib64/ld-linux-x86-64.so.2
Module_base_address=00002B07ABBBA000
Target=2_90_20201022_810 (Linux 3.10.0-1160.15.2.el7.x86_64)
CPU=amd64 (64 logical CPUs) (0x7ddd171000 RAM)
----------- Stack Backtrace -----------
(0x00002B07ABBD960E [ld-linux-x86-64.so.2+0x1f60e])
(0x00002B07ABBC4517 [ld-linux-x86-64.so.2+0xa517])
(0x00002B07ABBCFD37 [ld-linux-x86-64.so.2+0x15d37])
_dl_catch_exception+0x88 (0x00002B07ABFAA8B8 [libc.so.6+0x1638b8])
(0x00002B07ABBCF5FA [ld-linux-x86-64.so.2+0x155fa])
(0x00002B07ABE4234C [libdl.so.2+0x134c])
_dl_catch_exception+0x88 (0x00002B07ABFAA8B8 [libc.so.6+0x1638b8])
_dl_catch_error+0x33 (0x00002B07ABFAA983 [libc.so.6+0x163983])
(0x00002B07ABE42B59 [libdl.so.2+0x1b59])
dlopen+0x4a (0x00002B07ABE423DA [libdl.so.2+0x13da])
(0x00002B07ACFB1088 [libj9prt29.so+0x2e088])
(0x00002B07ACC64947 [libj9vm29.so+0x73947])
(0x00002B07ACC64F3D [libj9vm29.so+0x73f3d])
(0x00002B07ACC65179 [libj9vm29.so+0x74179])
(0x00002B07ACC7272B [libj9vm29.so+0x8172b])
(0x00002B07ACC6CD90 [libj9vm29.so+0x7bd90])
(0x00002B07ACCC34B2 [libj9vm29.so+0xd24b2])
---------------------------------------
JVMDUMP039I Processing dump event "gpf", detail "" at 2022/06/29 11:50:23 - please wait.
JVMDUMP032I JVM requested System dump using '/cleansumstats/outdir/core.20220629.115023.11959.0001.dmp' in response to an event
JVMPORT030W /proc/sys/kernel/core_pattern setting "|/usr/libexec/abrt-hook-ccpp %s %c %p %u %g %t e %P %I %h" specifies that the core dump is to be piped to an external program.  Attempting to rename either core or core.11380.

JVMDUMP010I System dump written to /cleansumstats/outdir/core.20220629.115023.11959.0001.dmp
JVMDUMP032I JVM requested Java dump using '/cleansumstats/outdir/javacore.20220629.115023.11959.0002.txt' in response to an event
JVMDUMP010I Java dump written to /cleansumstats/outdir/javacore.20220629.115023.11959.0002.txt
JVMDUMP032I JVM requested Snap dump using '/cleansumstats/outdir/Snap.20220629.115023.11959.0003.trc' in response to an event
JVMDUMP010I Snap dump written to /cleansumstats/outdir/Snap.20220629.115023.11959.0003.trc
JVMDUMP032I JVM requested JIT dump using '/cleansumstats/outdir/jitdump.20220629.115023.11959.0004.dmp' in response to an event
JVMDUMP010I JIT dump written to /cleansumstats/outdir/jitdump.20220629.115023.11959.0004.dmp
JVMDUMP013I Processed dump event "gpf", detail "".
[jesgaaopen@fe-open-01 raw_library]$
pappewaio commented 1 year ago

The reason for this error is when too many jobs use the same tmp and workdir.

Solve it by using -b and -w flags to create individual folders for each sumstat file to clean:

-b <dir>     path to system tmp or scratch (default: /tmp)
-w <dir>     path to workdir/intermediate files (default: work)