#30 runCorrection failed as `GOMP_4.0' not found

[Bright]

Hi!

When I run PBcR with demo in SGE, it failed in the step of correction. According to log, it was caused by using old gcc library. Although I had solve the same problem by re-make softlink (https://sourceforge.net/p/wgs-assembler/support-requests/29/), I can't use the same method as I don't have root priviledge. Also, I had add my library path to LD_LIBRARY_PATH, but it didn't work.

Any suggestion would be grateful!

Following is what I do:

1. Running PBcR
   PBcR -threads 20 -length 500 -partitions 200 -l lambdaIll -s pacbio.SGE.spec -fastq pacbio.filtered_subreads.fastq genomeSize=50000 illumina.frg >log/pbcr.log 2>log/pbcr.err
2. Tail log in templambdaIll/runPBcR.sge.out.05
   Error: found output from runCorrection. Stopping to avoid infinite loops. To try again, remove asm.layout.*
3. Log in templambdaIll/asm.layout.err
   /tools/wgs-8.3rc2/Linux-amd64/bin/correctPacBio: /usr/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by /tools/wgs-8.3rc2/Linux-amd64/bin/correctPacBio)
4. Check with ldd
   ldd /tools/wgs-8.3rc2/Linux-amd64/bin/correctPacBio
   linux-vdso.so.1 => (0x00007fff663ff000)
   libpthread.so.0 => /lib64/libpthread.so.0 (0x000000332f200000)
   libz.so.1 => /tools/zlib/destDir/lib/libz.so.1 (0x00007ffe6f8c3000)
   libstdc++.so.6 => /tools/gcc/destDir/lib64/libstdc++.so.6 (0x00007ffe6f535000)
   libm.so.6 => /lib64/libm.so.6 (0x000000332ea00000)
   libgomp.so.1 => /tools/gcc/destDir/lib64/libgomp.so.1 (0x00007ffe6f313000)
   libgcc_s.so.1 => /tools/gcc/destDir/lib64/libgcc_s.so.1 (0x00007ffe6f0fd000)
   libc.so.6 => /lib64/libc.so.6 (0x000000332e600000)
   /lib64/ld-linux-x86-64.so.2 (0x000000332e200000)
   librt.so.1 => /lib64/librt.so.1 (0x000000332fa00000)
   libdl.so.2 => /lib64/libdl.so.2 (0x000000332ee00000)
   ldd /usr/lib64/libgomp.so.1
   linux-vdso.so.1 => (0x00007fff25fff000)
   librt.so.1 => /lib64/librt.so.1 (0x000000332fa00000)
   libpthread.so.0 => /lib64/libpthread.so.0 (0x000000332f200000)
   libc.so.6 => /lib64/libc.so.6 (0x000000332e600000)
   /lib64/ld-linux-x86-64.so.2 (0x000000332e200000)
5. I had add the library path to LD_LIBRARY_PATH, but it didn't work
   echo $LD_LIBRARY_PATH
   /tools/boost/destDir/stage/lib:/tools/zlib/destDir/lib:/tools/gcc/destDir/lib64:/tools/gcc/gmp/destDir/lib:/tools/gcc/mpfr/destDir/lib:/tools/gcc/mpc/destDir/lib:/opt/gridengine/lib/lx26-amd64:/opt/openmpi/lib:/lib

[Bright]

This problm occur when I submit job to SGE, run in local wouldn't make trouble. It seemed when submitting to SGE, the LD_LIBRARY_PATH doesn't work?

[Bright]

I had solved this problem using the parameter "-V" (sed -i 's#qsub#qsub -V' PBcR). I want to close this tick, but I don't know how to close.