> From: Bart Nijsse [bart.nij...@wur.nl] > Sent: Thursday, October 09, 2014 9:42 AM > To: denovoassembler-users@lists.sourceforge.net > Subject: [Denovoassembler-users] Critical exception... memory exceeds the > CHUNK_SIZE > > > > > Dear Ray developers, > > I am trying to do a denovo assembly using Ray with 300bp paired end reads. > But I am receiving an error halfway of the run with the following command: > > mpiexec -n 28 /home/programs/assembly/Ray-2.3.1/Ray -k 101 -p read1.fastq > read2.fastq -o k_101 > > > Using different k-mers doesn't help. > > Critical exception: The length of the requested memory exceeds the > CHUNK_SIZE: 63958792 > 33554432 > Ray: RayPlatform/memory/MyAllocator.cpp:97: void* MyAllocator::allocate(int): > Assertion `false' failed. > [ssb5:01427] *** Process received signal *** > [ssb5:01427] Signal: Aborted (6) > [ssb5:01427] Signal code: (-6) > [ssb5:01427] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) > [0x7fd9ebb00340] > [ssb5:01427] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39) > [0x7fd9eb75ebb9] > [ssb5:01427] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) > [0x7fd9eb761fc8] > [ssb5:01427] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fa76) [0x7fd9eb757a76] > [ssb5:01427] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fb22) [0x7fd9eb757b22] > [ssb5:01427] [ 5] /home/programs/assembly/Ray-2.3.1/Ray() [0x544ece] > [ssb5:01427] [ 6] /home/programs/assembly/Ray-2.3.1/Ray() [0x4ff79f] > [ssb5:01427] [ 7] /home/programs/assembly/Ray-2.3.1/Ray() [0x567d20] > [ssb5:01427] [ 8] /home/programs/assembly/Ray-2.3.1/Ray() [0x56b29c] > [ssb5:01427] [ 9] /home/programs/assembly/Ray-2.3.1/Ray() [0x412936] > [ssb5:01427] [10] /home/programs/assembly/Ray-2.3.1/Ray() [0x40febc] > [ssb5:01427] [11] /home/programs/assembly/Ray-2.3.1/Ray() [0x40b902] > [ssb5:01427] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) > [0x7fd9eb749ec5] > [ssb5:01427] [13] /home/programs/assembly/Ray-2.3.1/Ray() [0x40d41f] > [ssb5:01427] *** End of error message *** > > > Any idea what might be causing the problem?
I never got that error before. Can you put the following lines (these are the addresses from your message) in a file named "Addresses.txt": 0x7fd9ebb00340 0x7fd9eb75ebb9 0x7fd9eb761fc8 0x7fd9eb757a76 0x7fd9eb757b22 0x544ece 0x4ff79f 0x567d20 0x56b29c 0x412936 0x40febc 0x40b902 0x7fd9eb749ec5 0x40d41f and then can you run this command: addr2line -e /home/programs/assembly/Ray-2.3.1/Ray < Addresses.txt This will tell us where this memory allocation is taking place. > > > Thanks in advance, > Bart Nijsse > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
