[GE users] qmake help

ksmagee magee at mayo.edu
Sun Mar 29 00:03:36 GMT 2009


Hello,

I'm attempting to get qmake to work in with the "make" parallel environment.  I have a set
of source code that compiles when I run 
qmake w/o specifying the "pe make", but
fails with the following message/core dump
when attempting to use the PE.  THe generated
core file is from
core.17531: ELF 64-bit LSB core file AMD x86-64, version 1 (SYSV), SVR4-style, from 'qrsh'


Any suggestions on how to debug further?


[magee at crick5 muscle3.7]$ qmake -q 1-hour -cwd -v PATH -l arch=lx24-amd64 -pe make 1-10 -v PATH-inherit -- all
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  aligngivenpath.cpp -o aligngivenpath.o
sunnode04.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  aligngivenpathsw.cpp -o aligngivenpathsw.o
wsnode10.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  aligntwomsas.cpp -o aligntwomsas.o
wsnode29.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  aligntwoprofs.cpp -o aligntwoprofs.o
wsnode09.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  aln.cpp -o aln.o
sunnode01.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  alpha.cpp -o alpha.o
wsnode46.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  anchors.cpp -o anchors.o
wsnode47.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  bittraceback.cpp -o bittraceback.o
wsnode50.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  blosum62.cpp -o blosum62.o
wsnode11.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  blosumla.cpp -o blosumla.o
wsnode08.mayo.edu
*** glibc detected *** qrsh: double free or corruption (out): 0x0000000016967160 ***
======= Backtrace: =========
/lib64/libc.so.6[0x368d471684]
/lib64/libc.so.6(cfree+0x8c)[0x368d474ccc]
/lib64/libpthread.so.0[0x368e00623b]
/lib64/libpthread.so.0(pthread_join+0xea)[0x368e00758a]
qrsh(cl_thread_join+0x48)[0x4d5b28]
qrsh(cl_thread_list_create_thread+0xb2)[0x4d6162]
qrsh(create_thread+0x1a)[0x42adba]
qrsh(do_server_loop+0xdf)[0x43d0df]
qrsh(main+0xc89)[0x422489]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x368d41d8b4]
qrsh(tcsetattr+0x4a)[0x4215ea]
======= Memory map: ========
00400000-0053a000 r-xp 00000000 00:15 162103315                          /home/sge6_2/bin/lx24-amd64/qsh
0063a000-0064b000 rwxp 0013a000 00:15 162103315                          /home/sge6_2/bin/lx24-amd64/qsh
0064b000-0064e000 rwxp 0064b000 00:00 0
16954000-16975000 rwxp 16954000 00:00 0
368cc00000-368cc1a000 r-xp 00000000 fd:00 6499                           /lib64/ld-2.5.so
368ce1a000-368ce1b000 r-xp 0001a000 fd:00 6499                           /lib64/ld-2.5.so
368ce1b000-368ce1c000 rwxp 0001b000 fd:00 6499                           /lib64/ld-2.5.so
368d400000-368d54a000 r-xp 00000000 fd:00 6500                           /lib64/libc-2.5.so
368d54a000-368d749000 ---p 0014a000 fd:00 6500                           /lib64/libc-2.5.so
368d749000-368d74d000 r-xp 00149000 fd:00 6500                           /lib64/libc-2.5.so
368d74d000-368d74e000 rwxp 0014d000 fd:00 6500                           /lib64/libc-2.5.so
368d74e000-368d753000 rwxp 368d74e000 00:00 0
368d800000-368d882000 r-xp 00000000 fd:00 6504                           /lib64/libm-2.5.so
368d882000-368da81000 ---p 00082000 fd:00 6504                           /lib64/libm-2.5.so
368da81000-368da82000 r-xp 00081000 fd:00 6504                           /lib64/libm-2.5.so
368da82000-368da83000 rwxp 00082000 fd:00 6504                           /lib64/libm-2.5.so
368dc00000-368dc02000 r-xp 00000000 fd:00 6501                           /lib64/libdl-2.5.so
368dc02000-368de02000 ---p 00002000 fd:00 6501                           /lib64/libdl-2.5.so
368de02000-368de03000 r-xp 00002000 fd:00 6501                           /lib64/libdl-2.5.so
368de03000-368de04000 rwxp 00003000 fd:00 6501                           /lib64/libdl-2.5.so
368e000000-368e015000 r-xp 00000000 fd:00 6502                           /lib64/libpthread-2.5.so
368e015000-368e214000 ---p 00015000 fd:00 6502                           /lib64/libpthread-2.5.so
368e214000-368e215000 r-xp 00014000 fd:00 6502                           /lib64/libpthread-2.5.so
368e215000-368e216000 rwxp 00015000 fd:00 6502                           /lib64/libpthread-2.5.so
368e216000-368e21a000 rwxp 368e216000 00:00 0
3692800000-369280d000 r-xp 00000000 fd:00 6506                           /lib64/libgcc_s-4.1.2-20080102.so.1
369280d000-3692a0d000 ---p 0000d000 fd:00 6506                           /lib64/libgcc_s-4.1.2-20080102.so.1
3692a0d000-3692a0e000 rwxp 0000d000 fd:00 6506                           /lib64/libgcc_s-4.1.2-20080102.so.1
3697200000-3697215000 r-xp 00000000 fd:00 6521                           /lib64/libnsl-2.5.so
3697215000-3697414000 ---p 00015000 fd:00 6521                           /lib64/libnsl-2.5.so
3697414000-3697415000 r-xp 00014000 fd:00 6521                           /lib64/libnsl-2.5.so
3697415000-3697416000 rwxp 00015000 fd:00 6521                           /lib64/libnsl-2.5.so
3697416000-3697418000 rwxp 3697416000 00:00 0
3697e00000-3697e11000 r-xp 00000000 fd:00 6511                           /lib64/libresolv-2.5.so
3697e11000-3698011000 ---p 00011000 fd:00 6511                           /lib64/libresolv-2.5.so
3698011000-3698012000 r-xp 00011000 fd:00 6511                           /lib64/libresolv-2.5.so
3698012000-3698013000 rwxp 00012000 fd:00 6511                           /lib64/libresolv-2.5.so
3698013000-3698015000 rwxp 3698013000 00:00 0
2afac5e94000-2afac5e95000 rwxp 2afac5e94000 00:00 0
2afac5ebf000-2afac5ec2000 rwxp 2afac5ebf000 00:00 0
2afac5ec2000-2afac5ecc000 r-xp 00000000 fd:00 6172                       /lib64/libnss_files-2.5.so
2afac5ecc000-2afac60cb000 ---p 0000a000 fd:00 6172                       /lib64/libnss_files-2.5.so
2afac60cb000-2afac60cc000 r-xp 00009000 fd:00 6172                       /lib64/libnss_files-2.5.so
2afac60cc000-2afac60cd000 rwxp 0000a000 fd:00 6172                       /lib64/libnss_files-2.5.so
2afac60cd000-2afac60d7000 r-xp 00000000 fd:00 6176                       /lib64/libnss_nis-2.5.so
2afac60d7000-2afac62d6000 ---p 0000a000 fd:00 6176                       /lib64/libnss_nis-2.5.so
2afac62d6000-2afac62d7000 r-xp 00009000 fd:00 6176                       /lib64/libnss_nis-2.5.so
2afac62d7000-2afac62d8000 rwxp 0000a000 fd:00 6176                       /lib64/libnss_nis-2.5.so
2afac6302000-2afac6306000 r-xp 00000000 fd:00 6170                       /lib64/libnss_dns-2.5.so
2afac6306000-2afac6505000 ---p 00004000 fd:00 6170                       /lib64/libnss_dns-2.5.so
2afac6505000-2afac6506000 r-xp 00003000 fd:00 6170                       /lib64/libnss_dns-2.5.so
2afac6506000-2afac6507000 rwxp 00004000 fd:00 6170                       /lib64/libnss_dns-2.5.so
2afb48000000-2afb48021000 rwxp 2afb48000000 00:00 0
2afb48021000-2afb4c000000 ---p 2afb48021000 00:00 0
7fffe4c00000-7fffe4c16000 rw-p 7fffe4c00000 00:00 0                      [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vdso]
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  clust.cpp -o clust.o
wsnode29.mayo.edu
g++ -c -O3 -funroll-loops -Winline -DNDEBUG=1  cluster.cpp -o cluster.o
wsnode46.mayo.edu
qmake: *** [aligngivenpathsw.o] Aborted (core dumped)
qmake: *** Waiting for unfinished jobs....
qmake: *** [clust.o] Segmentation fault (core dumped)

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