[blu78]

ok thanks again.
I will let you know any news and I will upgrade to the 0.6.4b.

All the best

[fennan]

It seems I am having the same problem...
I am using bfast-0.6.4 and I set the number of threads to 8 I got the "Segmentation fault" error. However when I set it to 4, BFAST works just fine. Was this problem solved?

Thanks!

[nilshomer]

It seems I am having the same problem...
I am using bfast-0.6.4 and I set the number of threads to 8 I got the "Segmentation fault" error. However when I set it to 4, BFAST works just fine. Was this problem solved?

Thanks!

Could you post the results of the "configure" command (during install)?

[cbarette]

Hi,

We have the same problem with debian Lenny 64bits: bfast (0.6.4d but also 0.6.2a and 0.6.3c) crashes when running with 8 CPU but not with 4 (our server has 32 cores so we would really want to use as many resources as possible.

- The configuration phase is the same as blue78 : http://pastebin.com/vW9kXwX9
- It generates the following config.h : http://pastebin.com/gk57XfP9
- and for the compilation: http://pastebin.com/jBLjyL2s (it complains a bit about gzread64 not being declared but nothing wrong during the linking)

We are running the folowwing commands:

WORK_DIR=/data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST
REF_GENOME=/data/ngs/annotations/bfast_indexes/hg19.fa
BFAST_BIN_DIR=/bioinfo/local/build/bfast_0.6.4d/bin
NB_THREADS=8

nohup $BFAST_BIN_DIR/bfast match -f $REF_GENOME -n $NB_THREADS -A 1 -r $WORK_DIR/FastQ/reads100000.200.fastq > $WORK_DIR/Bmf/bmfbfast.matches.file.hg19.200.bmf

The result is

************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /data/ngs/annotations/bfast_indexes/hg19.fa. 
Validating readsFileName /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq. 
Validating tmpDir path ./. 
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode:                            [ExecuteProgram]
fastaFileName:                          /data/ngs/annotations/bfast_indexes/hg19.fa
mainIndexes                             [Auto-recognizing]
secondaryIndexes                        [Not Using]
readsFileName:                          /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq
offsets:                                [Using All]
loadAllIndexes:                         [Not Using]
compression:                            [Not Using]
space:                                  [Color Space]
startReadNum:                           1
endReadNum:                             2147483647
keySize:                                [Not Using]
maxKeyMatches:                          8
maxNumMatches:                          384
whichStrand:                            [Both Strands]
numThreads:                             8
queueLength:                            250000
tmpDir:                                 ./
timing:                                 [Not Using]
************************************************************
Searching for main indexes...
Found 10 index (10 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.brg.
In total read 25 contigs for a total of 3095693983 bases
************************************************************
Reading /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq into a temp file.
Will process 100000 reads.
************************************************************
Searching index file 1/10 (index #1, bin #1)...
Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif.
Read index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif.
Reads processed: 100000
Cleaning up index.
Searching index file 1/10 (index #1, bin #1) complete...
Found 60065 matches.
************************************************************
Searching index file 2/10 (index #2, bin #1)...
Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.2.1.bif.

and the it crashes with a segfault.

We generated a core dump but the crash is in a function of libz so we installed the debug version of libz and here is the result: http://pastebin.com/Ae0re589

So if you have any leads, I would be happy to help and test.

Best regards

[nilshomer]

Thank-you for providing a good amount of info to help my debug. Googling the compiler warning, it may be the case that your zlib is buggy in Ubuntu (see my links hinting at that). The function "gzopen64" is declared in zlib to provide 64-bit support, but is not being declared correctly. I am guessing it crashes when trying to read in a compressed index (as shown by the last BFAST status message). In "configure.ac", could you change the "extended_CFLAGS" line to the below and see what happens?

extended_CFLAGS="-m64 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE";

The run "sh autogen.sh && ./configure && make".

Links:

http://groups.google.com/a/chromium.org/group/chromium-bugs/browse_thread/thread/b3517cdd0f29336c

http://lipyrary.blogspot.com/2009/08/libxml2-crash-on-64bit-ubuntu.html

http://bugs.gentoo.org/316377

http://code.google.com/p/chromium/issues/detail?id=38073

[cbarette]

Hi,

Thanks a lot for your feedback ! With this modification bfast runs perfectly with 8 threads.

Cheers