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【求助】Performing VASP: mpich2 someties breaks down 已有5人参与
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前面我发个同样的贴，可是问题没有得到解决。比较急，希望大家能够帮助下，谢谢! 我在RHEL 5.4; mpich2-1.2.1p1;pgi-9.0.1;双核Xeon E5504 (intel CPU)环境下跑并行的vasp。有些作业，能够正常并行计算（使用命令：mpiexec -n 8 vasp.pgi >out& or mpiexec -n 8 vasp.pgi out& or mpiexec -n 8 vasp.pgi ，有些作业却不能运行（我安装mpich2-1.2.p1), pgi.9.0.1没有问题），这时程序读了INCAR，POTCAR，POSCAR和KPOINTS文件后，屏幕提示如下的错误： ---------------------------------------------------------------------- running on 8 nodes distr: one band on 1 nodes, 8 groups vasp.4.6.21 23Feb03 complex POSCAR found : 3 types and 30 ions LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro POSCAR, INCAR and KPOINTS ok, starting setup WARNING: wrap around errors must be expected mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & FFT: planning ... 2 reading WAVECAR mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null mpiexec_qltang1 (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null & WARNING: random wavefunctions but no delay for mixing, default for NELMDL entering main loop N E dE d eps ncg rms rms(c) rank 6 in job 36 qltang1_54199 caused collective abort of all ranks exit status of rank 6: killed by signal 9 rank 3 in job 36 qltang1_54199 caused collective abort of all ranks exit status of rank 3: killed by signal 9 希望能得到帮助，谢谢！ |
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我感觉是stack size limit的问题 我又试了下gump_813276建议的在vasp源程序增加一个limit.c文件，按照修改方法，我在main.F中的这个位置： CHARACTER (LEN=5) IDENTIFY !-----parameters for sphpro.f INTEGER :: LDIMP,LMDIMP,LTRUNC=3 !======================================================================= ! All COMMON blocks !======================================================================= INTEGER IXMIN,IXMAX,IYMIN,IYMAX,IZMIN,IZMAX COMMON /WAVCUT/ IXMIN,IXMAX,IYMIN,IYMAX,IZMIN,IZMAX INTEGER ISYMOP,NROT,IGRPOP,NROTK,INVMAP,NPCELL REAL(q) GTRANS,AP REAL(q) RHOTOT(4) INTEGER(8) IL,I1,I2_0,I3,I4 #ifdef gammareal CHARACTER (LEN=*),PARAMETER :: VASP='vasp.4.6.21 13Feb03 gamma-only' #else CHARACTER (LEN=*),PARAMETER :: VASP='vasp.4.6.21 23Feb03 complex ' #endif COMMON /SYMM/ ISYMOP(3,3,48),NROT,IGRPOP(3,3,48),NROTK, & & GTRANS(3,48),INVMAP(48),AP(3,3),NPCELL !======================================================================= ! initialise / set constants and parameters ... !======================================================================= IO%LOPEN =.TRUE. ! open all files with file names IO%IU0 = 6 IO%IU6 = 8 #ifdef Fujitsu IO%IU5 = 7 #else IO%IU5 = 5 #endif !R.S tiu6 = IO%IU6 tiu0 = IO%IU0 IO%ICMPLX=ICMPLX IO%MRECL =MRECL PRED%ICMPLX=ICMPLX CALL stacksize() （注：这是新增加的行） CALL TIMING(0,UTIME,STIME,ETIME,MINPGF,MAJPGF, & & RSIZM,AVSIZ,ISWPS,IOOPS,IVCSW,IERR) IF (IERR/=0) ETIME=0._q ! switch off kill 然后编译串行vasp,得到二进制vasp文件。可执行测试算例时，同样VASP只读入输入文件就报这样的错误： [qltang@qltang1 pgi]$ !vasp vasp Before: cur=-1,hard=-1 After: res=0,cur=-1,hard=-1 vasp.4.6.21 23Feb03 complex POSCAR found : 3 types and 48 ions LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro POSCAR, INCAR and KPOINTS ok, starting setup WARNING: wrap around errors must be expected FFT: planning ... 16 reading WAVECAR entering main loop N E dE d eps ncg rms rms(c) *** glibc detected *** vasp: free(): invalid next size (fast): 0x0000000011c92760 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3fd74722ef] /lib64/libc.so.6(cfree+0x4b)[0x3fd747273b] vasp[0x4f6176] ======= Memory map: ======== 00400000-006bc000 r-xp 00000000 08:03 1770606 /usr/local/bin/vasp 008bb000-008e9000 rwxp 002bb000 08:03 1770606 /usr/local/bin/vasp 008e9000-00c32000 rwxp 008e9000 00:00 0 11bc5000-123cc000 rwxp 11bc5000 00:00 0 [heap] 3fd6c00000-3fd6c1c000 r-xp 00000000 08:03 3204371 /lib64/ld-2.5.so 3fd6e1b000-3fd6e1c000 r-xp 0001b000 08:03 3204371 /lib64/ld-2.5.so 3fd6e1c000-3fd6e1d000 rwxp 0001c000 08:03 3204371 /lib64/ld-2.5.so 3fd7400000-3fd754d000 r-xp 00000000 08:03 3204372 /lib64/libc-2.5.so 3fd754d000-3fd774d000 ---p 0014d000 08:03 3204372 /lib64/libc-2.5.so 3fd774d000-3fd7751000 r-xp 0014d000 08:03 3204372 /lib64/libc-2.5.so 3fd7751000-3fd7752000 rwxp 00151000 08:03 3204372 /lib64/libc-2.5.so 3fd7752000-3fd7757000 rwxp 3fd7752000 00:00 0 3fd7c00000-3fd7c82000 r-xp 00000000 08:03 3204376 /lib64/libm-2.5.so 3fd7c82000-3fd7e81000 ---p 00082000 08:03 3204376 /lib64/libm-2.5.so 3fd7e81000-3fd7e82000 r-xp 00081000 08:03 3204376 /lib64/libm-2.5.so 3fd7e82000-3fd7e83000 rwxp 00082000 08:03 3204376 /lib64/libm-2.5.so 3fd8000000-3fd8016000 r-xp 00000000 08:03 3204374 /lib64/libpthread-2.5.so 3fd8016000-3fd8215000 ---p 00016000 08:03 3204374 /lib64/libpthread-2.5.so 3fd8215000-3fd8216000 r-xp 00015000 08:03 3204374 /lib64/libpthread-2.5.so 3fd8216000-3fd8217000 rwxp 00016000 08:03 3204374 /lib64/libpthread-2.5.so 3fd8217000-3fd821b000 rwxp 3fd8217000 00:00 0 3fd8800000-3fd8807000 r-xp 00000000 08:03 3204377 /lib64/librt-2.5.so 3fd8807000-3fd8a07000 ---p 00007000 08:03 3204377 /lib64/librt-2.5.so 3fd8a07000-3fd8a08000 r-xp 00007000 08:03 3204377 /lib64/librt-2.5.so 3fd8a08000-3fd8a09000 rwxp 00008000 08:03 3204377 /lib64/librt-2.5.so 3fdd000000-3fdd00d000 r-xp 00000000 08:03 3202051 /lib64/libgcc_s-4.1.2-20080825.so.1 3fdd00d000-3fdd20d000 ---p 0000d000 08:03 3202051 /lib64/libgcc_s-4.1.2-20080825.so.1 3fdd20d000-3fdd20e000 rwxp 0000d000 08:03 3202051 /lib64/libgcc_s-4.1.2-20080825.so.1 2b2cd10a3000-2b2cd10a9000 rwxp 2b2cd10a3000 00:00 0 2b2cd10ca000-2b2ce4648000 rwxp 2b2cd10ca000 00:00 0 7fff16e0a000-7fff16e1f000 rwxp 7ffffffea000 00:00 0 [stack] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] Aborted (core dumped) [qltang@qltang1 pgi]$ 所以我想继续请教这个问题：我的问题出在哪里呢？和我装的rhel 5.4有关吗？ 谢谢！ |
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