It looks like Sean's problem is related to some sort of data corruption. The genome he's working with is 4 gig instead of the usual 3 gig. It looks like gfServer does report an error message about it already. We're still working to see where the data corruption came in. Meanwhile he's got gfServer up and running on a cleaned up version.
On Aug 14, 2009, at 1:09 PM, Jim Kent wrote: > Hi Sean - thanks for reporting the problems. We do have a gfServer > going on GRCh37 here, so I think there's hope of fixing the problem. > To start with the trouble-shooting let's make sure that it's not a > data corruption issue or a blat version issue. Could you send us the > results of running the md5sum program on the .2bit file and also the > GRCh37 genome that you downloaded? This will help us rule out data > corruption. Could you also try downloading a gfServer from our > current source tree and seeing if that does the same thing? I put up > a Linux 64 bit binary at http://hgwdev.cse.ucsc.edu/~kent/gfServer.gz. > > Take care, > Jim > > On Aug 14, 2009, at 7:53 AM, Sean O'Keeffe wrote: > >> Hi, >> We've had a local BLAT server (gfServer v32x1) running happily here ( >> 9GB main memory, 64 bit linux machine) for quiet some time with >> Human(NCBI36),Mouse(M37) and Yeast all running in parallel on >> different >> ports. >> Recently I downloaded and converted Human GRCh37 to 2bit format and >> tried to include it among the list and it worked fine. However, on >> starting gfClient, the new gfServer crashed immediately. I thought >> the >> memory may have been an issue and shut down all other server >> instances >> but no joy. On restart of only 1 server instance (GRCh37), gfClient >> crashed the server again. The following is spewed to STDOUT on crash: >> >> Any help would be great, thanks. >> Sean. >> >> *** glibc detected *** gfServer: double free or corruption (!prev): >> 0x0000000000772c80 *** >> ======= Backtrace: ========= >> /lib/libc.so.6[0x2add1c01e40d] >> /lib/libc.so.6(__libc_free+0x76)[0x2add1c020136] >> gfServer[0x4107a3] >> gfServer[0x410ee7] >> gfServer[0x410bb2] >> gfServer[0x410bcd] >> gfServer[0x406894] >> gfServer[0x407514] >> gfServer[0x407585] >> gfServer[0x402cbd] >> gfServer[0x403531] >> gfServer[0x403e1e] >> gfServer[0x40472d] >> /lib/libc.so.6(__libc_start_main+0xf4)[0x2add1bfcf4f4] >> gfServer[0x4027ba] >> ======= Memory map: ======== >> 00400000-00426000 r-xp 00000000 00:17 690043 >> /amd/kronecker/2/package/blat/33/x86_64/bin/gfServer >> 00525000-00527000 rw-p 00025000 00:17 690043 >> /amd/kronecker/2/package/blat/33/x86_64/bin/gfServer >> 00527000-02536000 rw-p 00527000 00:00 0 >> [heap] >> 2add1bd18000-2add1bd33000 r-xp 00000000 08:01 59332 >> /arch/x86_64/lib/ld-2.6.1.so >> 2add1bd33000-2add1bd35000 rw-p 2add1bd33000 00:00 0 >> 2add1bd40000-2add1bd41000 rw-p 2add1bd40000 00:00 0 >> 2add1be32000-2add1be33000 r--p 0001a000 08:01 59332 >> /arch/x86_64/lib/ld-2.6.1.so >> 2add1be33000-2add1be34000 rw-p 0001b000 08:01 59332 >> /arch/x86_64/lib/ld-2.6.1.so >> 2add1be34000-2add1beb1000 r-xp 00000000 08:01 59336 >> /arch/x86_64/lib/libm-2.6.1.so >> 2add1beb1000-2add1bfb0000 ---p 0007d000 08:01 59336 >> /arch/x86_64/lib/libm-2.6.1.so >> 2add1bfb0000-2add1bfb1000 r--p 0007c000 08:01 59336 >> /arch/x86_64/lib/libm-2.6.1.so >> 2add1bfb1000-2add1bfb2000 rw-p 0007d000 08:01 59336 >> /arch/x86_64/lib/libm-2.6.1.so >> 2add1bfb2000-2add1c0ea000 r-xp 00000000 08:01 59333 >> /arch/x86_64/lib/libc-2.6.1.so >> 2add1c0ea000-2add1c1e9000 ---p 00138000 08:01 59333 >> /arch/x86_64/lib/libc-2.6.1.so >> 2add1c1e9000-2add1c1ed000 r--p 00137000 08:01 59333 >> /arch/x86_64/lib/libc-2.6.1.so >> 2add1c1ed000-2add1c1ee000 rw-p 0013b000 08:01 59333 >> /arch/x86_64/lib/libc-2.6.1.so >> 2add1c1ee000-2add9cee9000 rw-p 2add1c1ee000 00:00 0 >> 2add9cef5000-2add9cf02000 r-xp 00000000 08:01 36886 >> /arch/x86_64/usr/lib/libgcc_s.so.1 >> 2add9cf02000-2add9d001000 ---p 0000d000 08:01 36886 >> /arch/x86_64/usr/lib/libgcc_s.so.1 >> 2add9d001000-2add9d002000 rw-p 0000c000 08:01 36886 >> /arch/x86_64/usr/lib/libgcc_s.so.1 >> 2adda0000000-2adda0021000 rw-p 2adda0000000 00:00 0 >> 2adda0021000-2adda4000000 ---p 2adda0021000 00:00 0 >> 7fff8ed7c000-7fff8ed91000 rw-p 7ffffffea000 00:00 0 >> [stack] >> 7fff8edfe000-7fff8ee00000 r-xp 7fff8edfe000 00:00 0 >> [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 >> [vsyscall] >> >> [1] Abort gfServer start >> genome.molgen.mpg.de >> 17782 >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
