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
