Hi,
Thanks a lot for your feedback ! With this modification bfast runs perfectly with 8 threads.
Cheers
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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".
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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:
The result isCode: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
and the it crashes with a segfault.Code:************************************************************ 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.
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 regardsLast edited by cbarette; 08-02-2010, 07:31 AM.Leave a comment:
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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!Leave a comment:
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I don't have any new leads. Most users I know run with 8-threads on all parts of BFAST. Maybe there is a memory bus issue that is causing it to crash since there are too many threads trying to access memory. This seems unlikely and is difficult to prove. Stick with your four threads and we'll see if any other users experience the same thing,Originally posted by blu78 View Post
NilsLeave a comment:
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Hi,
I am using Linux Debian 64 bit.
Here is the output of configure. Thanks for all your help.
Code:$ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for a BSD-compatible install... /usr/bin/install -c ./configure: line 3462: git: command not found checking for BZ2_bzRead in -lbz2... yes checking for an ANSI C-conforming const... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for pow in -lm... yes checking for gzread in -lz... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strpbrk... yes checking for strstr... yes checking for strtok_r... yes checking for int8_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for short int... yes checking size of short int... 2 checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 8 checking for ANSI C header files... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inline... inline configure: creating ./config.status config.status: creating Makefile config.status: creating bfast/Makefile config.status: creating butil/Makefile config.status: creating scripts/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands
Last edited by blu78; 04-11-2010, 09:49 AM.Leave a comment:
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Hi, I think I have a bit more information on this problem.
I tried to rerun the smaller example with 4 cores instead of 8 (i.e. -n 4) and apparently the Segmentation Fault problem is solved.
The box I was running bfast on has eight cores, theoretically should I set -n 8? Does this parameter need to be a power of 2?
At the moment I am trying to run the bigger example with 4 cores. I will fill you in as soon as I will know the result of this computation.
ThanksLeave a comment:
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I apologize for your experience so far. The best way to move forward is to email me the reference and reads, and then I can quickly debug myself to see if their is a bug in the program or a configuration issue. What does the "F3_10Mchunk.qfasta" file look like?Originally posted by blu78 View PostLeave a comment:
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