You have too many sequences (695 318 412 sequences) for the available memory (49554300 kB).
The git version of Ray provides a better adaptive Bloom filter that reduces memory usage caused by erroneous k-mers, but in your case I think you need to stack up more machines. Also important, what is the estimated genome length ? On 02/19/2013 07:44 AM, frederic texier wrote: > I don't know if it's that. I can't see more. > > Rank 5: assembler memory usage: 6190616 KiB > Rank 1 has 39700000 vertices > Rank 1: assembler memory usage: 6190616 KiB > Rank 5 is counting k-mers in sequence reads [1860001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1546 units/second > Estimated remaining time for this step: 15 hours, 16 minutes, 56 seconds > Rank 4 is counting k-mers in sequence reads [1830001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1567 units/second > Estimated remaining time for this step: 15 hours, 4 minutes, 57 seconds > Rank 7 is counting k-mers in sequence reads [1900001/86914805] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1584 units/second > Estimated remaining time for this step: 14 hours, 54 minutes, 30 seconds > Rank 2 has 39800000 vertices > Rank 2: assembler memory usage: 6194904 KiB > Rank 3 has 39800000 vertices > Rank 3: assembler memory usage: 6194904 KiB > Rank 0 has 39800000 vertices > Rank 0: assembler memory usage: 6194904 KiB > Rank 7 has 39800000 vertices > Rank 7: assembler memory usage: 6198988 KiB > Rank 4 has 39800000 vertices > Rank 4: assembler memory usage: 6194904 KiB > Rank 6 has 39800000 vertices > Rank 6: assembler memory usage: 6199000 KiB > Rank 5 has 39800000 vertices > Rank 5: assembler memory usage: 6194904 KiB > Rank 1 has 39800000 vertices > Rank 1: assembler memory usage: 6194904 KiB > Rank 6 is counting k-mers in sequence reads [1860001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1516 units/second > Estimated remaining time for this step: 15 hours, 35 minutes, 4 seconds > Rank 2 has 39900000 vertices > Rank 2: assembler memory usage: 6199192 KiB > Rank 3 has 39900000 vertices > Rank 3: assembler memory usage: 6199192 KiB > Rank 0 has 39900000 vertices > Rank 0: assembler memory usage: 6199192 KiB > Rank 1 is counting k-mers in sequence reads [1860001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1529 units/second > Estimated remaining time for this step: 15 hours, 27 minutes, 7 seconds > Rank 7 has 39900000 vertices > Rank 7: assembler memory usage: 6203276 KiB > Rank 6 has 39900000 vertices > Rank 6: assembler memory usage: 6203288 KiB > Rank 4 has 39900000 vertices > Rank 4: assembler memory usage: 6199192 KiB > Rank 5 has 39900000 vertices > Rank 5: assembler memory usage: 6199192 KiB > Rank 1 has 39900000 vertices > Rank 1: assembler memory usage: 6199192 KiB > Rank 3 is counting k-mers in sequence reads [1830001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1484 units/second > Estimated remaining time for this step: 15 hours, 55 minutes, 34 seconds > Rank 0 is counting k-mers in sequence reads [1820001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1540 units/second > Estimated remaining time for this step: 15 hours, 20 minutes, 56 seconds > Rank 2 is counting k-mers in sequence reads [1850001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1580 units/second > Estimated remaining time for this step: 14 hours, 57 minutes, 18 seconds > Rank 2 has 40000000 vertices > Rank 2: assembler memory usage: 6203480 KiB > Rank 3 has 40000000 vertices > Rank 3: assembler memory usage: 6199192 KiB > Rank 0 has 40000000 vertices > Rank 0: assembler memory usage: 6199192 KiB > Rank 7 has 40000000 vertices > Rank 7: assembler memory usage: 6207564 KiB > Rank 6 has 40000000 vertices > Rank 6: assembler memory usage: 6207576 KiB > Rank 4 has 40000000 vertices > Rank 4: assembler memory usage: 6203480 KiB > Rank 5 has 40000000 vertices > Rank 5: assembler memory usage: 6203480 KiB > Rank 1 has 40000000 vertices > Rank 1: assembler memory usage: 6199192 KiB > Rank 5 is counting k-mers in sequence reads [1870001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1520 units/second > Estimated remaining time for this step: 15 hours, 32 minutes, 30 seconds > Rank 4 is counting k-mers in sequence reads [1840001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1563 units/second > Estimated remaining time for this step: 15 hours, 7 minutes, 10 seconds > Rank 7 is counting k-mers in sequence reads [1910001/86914805] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1602 units/second > Estimated remaining time for this step: 14 hours, 44 minutes, 21 seconds > Rank 2 has 40100000 vertices > Rank 2: assembler memory usage: 6203480 KiB > Rank 3 has 40100000 vertices > Rank 3: assembler memory usage: 6203480 KiB > Rank 0 has 40100000 vertices > Rank 0: assembler memory usage: 6203480 KiB > Rank 7 has 40100000 vertices > Rank 7: assembler memory usage: 6207564 KiB > Rank 4 has 40100000 vertices > Rank 4: assembler memory usage: 6203480 KiB > Rank 6 has 40100000 vertices > Rank 6: assembler memory usage: 6207576 KiB > Rank 5 has 40100000 vertices > Rank 5: assembler memory usage: 6203480 KiB > Rank 1 has 40100000 vertices > Rank 1: assembler memory usage: 6207768 KiB > Rank 6 is counting k-mers in sequence reads [1870001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1517 units/second > Estimated remaining time for this step: 15 hours, 34 minutes, 21 seconds > Rank 2 has 40200000 vertices > Rank 2: assembler memory usage: 6207768 KiB > Rank 3 has 40200000 vertices > Rank 3: assembler memory usage: 6207768 KiB > Rank 0 has 40200000 vertices > Rank 0: assembler memory usage: 6207768 KiB > Rank 1 is counting k-mers in sequence reads [1870001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1497 units/second > Estimated remaining time for this step: 15 hours, 46 minutes, 50 seconds > Rank 7 has 40200000 vertices > Rank 7: assembler memory usage: 6211852 KiB > Rank 6 has 40200000 vertices > Rank 6: assembler memory usage: 6211864 KiB > Rank 4 has 40200000 vertices > Rank 4: assembler memory usage: 6207768 KiB > Rank 5 has 40200000 vertices > Rank 5: assembler memory usage: 6207768 KiB > Rank 1 has 40200000 vertices > Rank 1: assembler memory usage: 6207768 KiB > Rank 3 is counting k-mers in sequence reads [1840001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1466 units/second > Estimated remaining time for this step: 16 hours, 7 minutes, 11 seconds > Rank 0 is counting k-mers in sequence reads [1830001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1485 units/second > Estimated remaining time for this step: 15 hours, 54 minutes, 56 seconds > Rank 2 is counting k-mers in sequence reads [1860001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1516 units/second > Estimated remaining time for this step: 15 hours, 35 minutes, 4 seconds > Rank 2 has 40300000 vertices > Rank 2: assembler memory usage: 6212056 KiB > Rank 3 has 40300000 vertices > Rank 3: assembler memory usage: 6212056 KiB > Rank 0 has 40300000 vertices > Rank 0: assembler memory usage: 6212056 KiB > Rank 7 has 40300000 vertices > Rank 7: assembler memory usage: 6216140 KiB > Rank 5 has 40300000 vertices > Rank 5: assembler memory usage: 6212056 KiB > Rank 6 has 40300000 vertices > Rank 6: assembler memory usage: 6216152 KiB > Rank 4 has 40300000 vertices > Rank 4: assembler memory usage: 6212056 KiB > Rank 1 has 40300000 vertices > Rank 1: assembler memory usage: 6212056 KiB > Rank 5 is counting k-mers in sequence reads [1880001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1495 units/second > Estimated remaining time for this step: 15 hours, 47 minutes, 59 seconds > Rank 4 is counting k-mers in sequence reads [1850001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1436 units/second > Estimated remaining time for this step: 16 hours, 27 minutes, 17 seconds > Rank 7 is counting k-mers in sequence reads [1920001/86914805] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1489 units/second > Estimated remaining time for this step: 15 hours, 51 minutes, 21 seconds > Rank 2 has 40400000 vertices > Rank 2: assembler memory usage: 6216344 KiB > Rank 3 has 40400000 vertices > Rank 3: assembler memory usage: 6216344 KiB > Rank 0 has 40400000 vertices > Rank 0: assembler memory usage: 6216344 KiB > Rank 7 has 40400000 vertices > Rank 7: assembler memory usage: 6220428 KiB > Rank 6 has 40400000 vertices > Rank 6: assembler memory usage: 6220440 KiB > Rank 5 has 40400000 vertices > Rank 5: assembler memory usage: 6216344 KiB > Rank 4 has 40400000 vertices > Rank 4: assembler memory usage: 6216344 KiB > Rank 1 has 40400000 vertices > Rank 1: assembler memory usage: 6216344 KiB > Rank 6 is counting k-mers in sequence reads [1880001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1522 units/second > Estimated remaining time for this step: 15 hours, 31 minutes, 10 seconds > Rank 1 is counting k-mers in sequence reads [1880001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1474 units/second > Estimated remaining time for this step: 16 hours, 1 minutes, 29 seconds > Rank 2 has 40500000 vertices > Rank 2: assembler memory usage: 6216344 KiB > Rank 3 has 40500000 vertices > Rank 3: assembler memory usage: 6216344 KiB > Rank 0 has 40500000 vertices > Rank 0: assembler memory usage: 6216344 KiB > Rank 7 has 40500000 vertices > Rank 7: assembler memory usage: 6220428 KiB > Rank 6 has 40500000 vertices > Rank 6: assembler memory usage: 6224728 KiB > Rank 4 has 40500000 vertices > Rank 4: assembler memory usage: 6216344 KiB > Rank 5 has 40500000 vertices > Rank 5: assembler memory usage: 6216344 KiB > Rank 1 has 40500000 vertices > Rank 1: assembler memory usage: 6216344 KiB > Rank 3 is counting k-mers in sequence reads [1850001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1342 units/second > Estimated remaining time for this step: 17 hours, 36 minutes, 26 seconds > Rank 0 is counting k-mers in sequence reads [1840001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1322 units/second > Estimated remaining time for this step: 17 hours, 52 minutes, 33 seconds > Rank 2 is counting k-mers in sequence reads [1870001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1399 units/second > Estimated remaining time for this step: 16 hours, 53 minutes, 9 seconds > Rank 2 has 40600000 vertices > Rank 2: assembler memory usage: 6220632 KiB > Rank 3 has 40600000 vertices > Rank 3: assembler memory usage: 6220632 KiB > Rank 0 has 40600000 vertices > Rank 0: assembler memory usage: 6220632 KiB > Rank 7 has 40600000 vertices > Rank 7: assembler memory usage: 6224716 KiB > Rank 6 has 40600000 vertices > Rank 6: assembler memory usage: 6224728 KiB > Rank 5 has 40600000 vertices > Rank 5: assembler memory usage: 6220632 KiB > Rank 4 has 40600000 vertices > Rank 4: assembler memory usage: 6220632 KiB > Rank 1 has 40600000 vertices > Rank 1: assembler memory usage: 6220632 KiB > Rank 5 is counting k-mers in sequence reads [1890001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1290 units/second > Estimated remaining time for this step: 18 hours, 18 minutes, 30 seconds > Rank 4 is counting k-mers in sequence reads [1860001/86914801] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1324 units/second > Estimated remaining time for this step: 17 hours, 50 minutes, 40 seconds > Rank 7 is counting k-mers in sequence reads [1930001/86914805] > Speed RAY_SLAVE_MODE_ADD_VERTICES 1353 units/second > Estimated remaining time for this step: 17 hours, 26 minutes, 52 seconds > Rank 2 has 40700000 vertices > Rank 2: assembler memory usage: 6224920 KiB > Rank 3 has 40700000 vertices > Rank 3: assembler memory usage: 6224920 KiB > Rank 0 has 40700000 vertices > Rank 0: assembler memory usage: 6224920 KiB > Rank 7 has 40700000 vertices > Rank 7: assembler memory usage: 6229004 KiB > Rank 6 has 40700000 vertices > Rank 6: assembler memory usage: 6229016 KiB > Rank 5 has 40700000 vertices > Rank 5: assembler memory usage: 6224920 KiB > Rank 4 has 40700000 vertices > Rank 4: assembler memory usage: 6224920 KiB > Rank 1 has 40700000 vertices > Rank 1: assembler memory usage: 6224920 KiB > > > -----Message d'origine----- > De : Sébastien Boisvert [mailto:[email protected]] > Envoyé : mardi 19 février 2013 13:29 > À : frederic texier > Cc : [email protected] > Objet : Re: Ray bad termination > > On 02/19/2013 07:28 AM, frederic texier wrote: >> I have 49554300 kB physical memory. >> 695 318 412 sequences are in those files. >> >> You think I don't have enough physical memory for this number of sequences. >> > > In the standard output, what was the memory usage reported by Ray ? > >> >> Frederic. >> >> >> -----Message d'origine----- >> De : Sébastien Boisvert [mailto:[email protected]] >> Envoyé : mardi 19 février 2013 13:19 >> À : frederic texier >> Cc : [email protected] >> Objet : Re: Ray bad termination >> >> How much physical memory does your system have (head -n 1 /proc/meminfo) ? >> >> How many sequences are in those files (tail -n 3 >> ray_hiseq/NumberOfSequences.txt) ? >> >> On 02/19/2013 04:13 AM, frederic texier wrote: >>> Hi, >>> >>> I have an error when I launch an analysis with Ray. >>> >>> The following message appears: >>> >>> ===================================================================================== >>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >>> = EXIT CODE: 9 >>> = CLEANING UP REMAINING PROCESSES >>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >>> ===================================================================== >>> = =============== APPLICATION TERMINATED WITH THE EXIT STRING: Killed >>> (signal 9) >>> >>> Could you help me , please? >>> I don't know if it's a problem of memory or another problem. >>> >>> Best regards, >>> Frédéric. >>> >>> >> > ------------------------------------------------------------------------------ Everyone hates slow websites. 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