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#104 exact-p-val on high resolution data
exact-p-val throws a segmentation fault on high resolution data when
--exact-p-value=T
--mz-bin-width=0.1
--mz-bin-offset=0.05
and the error message:
scan 0 m/z 692.308778 charge 2 neutral mass 1382.603003
*** glibc detected *** /net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux: double free or corruption (out): 0x0000000011b28b80 ***
======= Backtrace: =========
/lib64/libc.so.6[0x39664760e6]
/lib64/libc.so.6[0x3966478c13]
/net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux(_ZN21TideSearchApplication6searchEPKSt6vectorIN18SpectrumCollection10SpecChargeESaIS2_EEP18ActivePeptideQueueRKS0_IPKN2pb7ProteinESaISC_EEd12_window_typeddiiiiidP11OutputFilesPSt14basic_ofstreamIcSt11char_traitsIcEESO_b+0x115c)[0x9dd784]
/net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux(_ZN21TideSearchApplication4mainEiPPc+0xe5b)[0x9dc0a3]
/net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux(_ZN19CruxApplicationList4mainEiPPc+0xf3)[0x927803]
/net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux(main+0x404)[0x898428]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x396641ecdd]
/net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux[0x897f71]
======= Memory map: ========
00400000-01321000 r-xp 00000000 00:29 4176069650 /net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux
01521000-015b4000 rw-p 00f21000 00:29 4176069650 /net/noble/vol2/home/kfattila/proj/crux-pval/src/c/crux
015b4000-0fb75000 rw-p 00000000 00:00 0
10a9c000-11f45000 rw-p 00000000 00:00 0 [heap]
3966000000-3966020000 r-xp 00000000 fd:00 918437 /lib64/ld-2.12.so
396621f000-3966220000 r--p 0001f000 fd:00 918437 /lib64/ld-2.12.so
3966220000-3966221000 rw-p 00020000 fd:00 918437 /lib64/ld-2.12.so
3966221000-3966222000 rw-p 00000000 00:00 0
3966400000-396658a000 r-xp 00000000 fd:00 920297 /lib64/libc-2.12.so
396658a000-3966789000 ---p 0018a000 fd:00 920297 /lib64/libc-2.12.so
3966789000-396678d000 r--p 00189000 fd:00 920297 /lib64/libc-2.12.so
396678d000-396678e000 rw-p 0018d000 fd:00 920297 /lib64/libc-2.12.so
396678e000-3966793000 rw-p 00000000 00:00 0
3966800000-3966883000 r-xp 00000000 fd:00 942912 /lib64/libm-2.12.so
3966883000-3966a82000 ---p 00083000 fd:00 942912 /lib64/libm-2.12.so
3966a82000-3966a83000 r--p 00082000 fd:00 942912 /lib64/libm-2.12.so
3966a83000-3966a84000 rw-p 00083000 fd:00 942912 /lib64/libm-2.12.so
3966c00000-3966c02000 r-xp 00000000 fd:00 942917 /lib64/libdl-2.12.so
3966c02000-3966e02000 ---p 00002000 fd:00 942917 /lib64/libdl-2.12.so
3966e02000-3966e03000 r--p 00002000 fd:00 942917 /lib64/libdl-2.12.so
3966e03000-3966e04000 rw-p 00003000 fd:00 942917 /lib64/libdl-2.12.so
3967000000-3967017000 r-xp 00000000 fd:00 942916 /lib64/libpthread-2.12.so
3967017000-3967217000 ---p 00017000 fd:00 942916 /lib64/libpthread-2.12.so
3967217000-3967218000 r--p 00017000 fd:00 942916 /lib64/libpthread-2.12.so
3967218000-3967219000 rw-p 00018000 fd:00 942916 /lib64/libpthread-2.12.so
3967219000-396721d000 rw-p 00000000 00:00 0
3967800000-3967807000 r-xp 00000000 fd:00 942932 /lib64/librt-2.12.so
3967807000-3967a06000 ---p 00007000 fd:00 942932 /lib64/librt-2.12.so
3967a06000-3967a07000 r--p 00006000 fd:00 942932 /lib64/librt-2.12.so
3967a07000-3967a08000 rw-p 00007000 fd:00 942932 /lib64/librt-2.12.so
7f1420bb2000-7f1420eb2000 rwxp 00000000 00:00 0
7f1420eb2000-7f1420eb9000 rw-p 00000000 00:00 0
7f1420eb9000-7f1420ece000 r-xp 00000000 00:2a 3570148218 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1
7f1420ece000-7f14210cd000 ---p 00015000 00:2a 3570148218 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1
7f14210cd000-7f14210ce000 rw-p 00014000 00:2a 3570148218 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1
7f14210ce000-7f14211b4000 r-xp 00000000 00:2a 1642740577 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.16
7f14211b4000-7f14213b3000 ---p 000e6000 00:2a 1642740577 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.16
7f14213b3000-7f14213bb000 r--p 000e5000 00:2a 1642740577 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.16
7f14213bb000-7f14213bd000 rw-p 000ed000 00:2a 1642740577 /net/gs/vol3/software/modules-sw/gcc/4.6.2/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.16
7f14213bd000-7f14213d3000 rw-p 00000000 00:00 0
7f14213d3000-7f14213d5000 r-xp 00000000 00:2a 1877600679 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_system.so.1.52.0
7f14213d5000-7f14215d5000 ---p 00002000 00:2a 1877600679 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_system.so.1.52.0
7f14215d5000-7f14215d6000 rw-p 00002000 00:2a 1877600679 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_system.so.1.52.0
7f14215d6000-7f14215eb000 r-xp 00000000 00:2a 835424240 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_filesystem.so.1.52.0
7f14215eb000-7f14217eb000 ---p 00015000 00:2a 835424240 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_filesystem.so.1.52.0
7f14217eb000-7f14217ec000 rw-p 00015000 00:2a 835424240 /net/gs/vol3/software/modules-sw/boost/1.52.0/Linux/RHEL6/x86_64/lib/libboost_filesystem.so.1.52.0
7f14217ec000-7f14217ed000 rw-p 00000000 00:00 0
7f1421807000-7f1421813000 rw-p 00000000 00:00 0
7fffa05f2000-7fffa060a000 rw-p 00000000 00:00 0 [stack]
7fffa0780000-7fffa0781000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
./runall_bn: line 144: 29842 Aborted (core dumped) $CRUX $searchTool --parameter-file $parameters --output-dir $outputdir $ms2 $indexDir
-bash-4.1$
Related
The mz-bin-width and mz-bin-offset parameters are not relevant to
tide-search. They only work for search-for-matches. You should get
identical results (and, presumably, the same seg fault) if you eliminate
those parameters.
Bill
On Wed, Jan 22, 2014 at 4:46 PM, Attila Kertesz-Farkas kfattila@users.sf.net wrote:
Related
Issues: #104
Jeff's exact p-value changes add those two parameters to tide-search, although they don't do anything when exact-p-value=F (as far as I understand it).
Yes, That's right. these two parameters are used only in exact-p-val search.
I've been through the p-value code, and I have a rough idea of where the problems are. In brief, there are a number of places where whole-integer binning of mass is implicitly assumed; this is certain to conflict with values of bin-width which imply otherwise. We're going to have to rethink how we get theoretical masses fed in from Tide, as well. Right now, these are also produced as whole-integer values.
I have reproduced the seg fault in the standalone version of the p-value code by setting binWidth < 1.0. The problem has nothing to do with the Tide integration per se.