Hi, I compiled GROMACS for Blue Gene/L, 'mdrun' seems to be working fine using a .tpr from a locally built linux version of GROMACS. However, 'grompp' fails with a segmentation fault and the following output:
Summary: program........................../home/ysmall/gromacs-3.3.1/Install_bgl/bin/grompp_smpi ended with software signal.......0x0000000b (SIGSEGV - segmentation violation) generated by interrupt...........0x00000002 (data storage interrupt) while executing instruction at...0x0023d45c dereferencing memory at..........0x00000000 General Purpose Registers: r00=0x0023d458 r01=0x1ffb3af0 r02=0xdeadbeef r03=0x00000000 r04=0x1ffb2ae0 r05=0x00000009 r06=0xfefefeff r07=0x7f7f7f7f r08=0x80808080 r09=0x00000000 r10=0x80808080 r11=0x00000000 r12=0x24000022 r13=0xdeadbeef r14=0x00388190 r15=0x00388188 r16=0x004125dc r17=0x004125ec r18=0x0045fbd0 r19=0x0045f920 r20=0x00000001 r21=0x00000000 r22=0x1ffb7fc0 r23=0x004125d8 r24=0x00410000 r25=0x00410000 r26=0x00413e18 r27=0x00466870 r28=0x003a5c94 r29=0x00000000 r30=0x00000000 r31=0x003a5a90 Special Purpose Registers: lr=0x0023d458 cr=0x84000024 xer=0x20000002 ctr=0x00000000 msr=0x0002f900 dear=0x00000000 esr=0x00000000 fpscr=0x82002000 dbcr0=0x00000000 dbsr=0x00000000 ccr0=0x00002000 sprg1=0x00080000 sprg2=0x00000000 sprg3=0x1ffb2ae0 sprg6=0x00000000 sprg7=0x00000000 Floating Point Registers: fpr0=0x00000000 00000000 00000000 00000000 fpr1=0x00000000 00000000 00000000 00000000 fpr2=0x00000000 00000000 00000000 00000000 fpr3=0x00000000 00000000 00000000 00000000 fpr4=0x00000000 00000000 00000000 00000000 fpr5=0x696e5f73 6600326d 00000000 3ff00000 fpr6=0x726f6d70 696e2f67 676c2f62 6c6c5f62 fpr7=0x6e737461 2e312f49 2d332e33 6d616373 fpr8=0x31360042 2d6e7000 74707200 5f31362e fpr9=0x70695f31 705f736d 726f6d70 6c6c2f67 fpr10=0x00000000 00000000 00000000 00000000 fpr11=0x79736d61 7666732f 6f002f70 726f002d fpr12=0x00000000 00000000 00000000 00000000 fpr13=0x00000000 5a453d31 495f5349 474c4d50 fpr14=0xffffffff ffffffff ffffffff ffffffff fpr15=0xffffffff ffffffff ffffffff ffffffff fpr16=0xffffffff ffffffff ffffffff ffffffff fpr17=0xffffffff ffffffff ffffffff ffffffff fpr18=0xffffffff ffffffff ffffffff ffffffff fpr19=0xffffffff ffffffff ffffffff ffffffff fpr20=0xffffffff ffffffff ffffffff ffffffff fpr21=0xffffffff ffffffff ffffffff ffffffff fpr22=0xffffffff ffffffff ffffffff ffffffff fpr23=0xffffffff ffffffff ffffffff ffffffff fpr24=0xffffffff ffffffff ffffffff ffffffff fpr25=0xffffffff ffffffff ffffffff ffffffff fpr26=0xffffffff ffffffff ffffffff ffffffff fpr27=0xffffffff ffffffff ffffffff ffffffff fpr28=0xffffffff ffffffff ffffffff ffffffff fpr29=0xffffffff ffffffff ffffffff ffffffff fpr30=0xffffffff ffffffff ffffffff ffffffff fpr31=0xffffffff ffffffff 00000000 00000000 Memory: stack top........................0x1ffc0000 stack frame pointer..............0x1ffb3af0 end of heap......................0x00c86000 start of program.................0x00200000 brk() failed w/ ENOMEM...........0 time(s) Personality: XYZT Coordinates.................0, 0, 0, 0 MPI Rank.........................0 mode.............................coprocessor job id...........................130333 Interrupt History: number of interrupts.............127 current timebase.................00000003647cfb0e TB=000000036474070c iar=003441c0 sp=1ffb38d0 value=000000c5 (system call interrupt) TB=0000000364742b0c iar=00362e74 sp=1ffb3800 value=0000002d (system call interrupt) TB=00000003647432f4 iar=003441f0 sp=1ffb3970 value=00000003 (system call interrupt) TB=000000036474ff2c iar=003441f0 sp=1ffb3970 value=00000003 (system call interrupt) TB=0000000364751ce0 iar=003441e0 sp=1ffb39c0 value=00000006 (system call interrupt) TB=0000000364754d94 iar=00362e74 sp=1ffb3910 value=0000002d (system call interrupt) TB=0000000364756d38 iar=00362c04 sp=1ffb26d0 value=0000007a (system call interrupt) TB=0000000364757c99 iar=0023d45c sp=1ffb3af0 value=00000000 (data storage interrupt) DCRs: DCR BGL_TSDCR_RE_SND_XP = 0 DCR BGL_TSDCR_RE_SND_XM = 0 DCR BGL_TSDCR_RE_SND_YP = 0 DCR BGL_TSDCR_RE_SND_YM = 0 DCR BGL_TSDCR_RE_SND_ZP = 0 DCR BGL_TSDCR_RE_SND_ZM = 0 Function Call Chain: 0x0023d45c 0x002392b0 0x002136fc 0x00219440 0x002001e4 End of stack I recompiled grompp with and without mpi enabled and with a variety of optimization options (-g O2, -g O, etc.) but the jobs still die with segmentation fault errors. Any suggestions? Thanks in advance for your help, Yolanda _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
