valgrind is unhappy with nss_lookup, but you can ignore these. They are not your error.<br><br> Matt<br><br><div class="gmail_quote">On Tue, May 5, 2009 at 4:46 PM, (Rebecca) Xuefei YUAN <span dir="ltr"><<a href="mailto:xy2102@columbia.edu">xy2102@columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
I am using valgrind to check the memory leaking and it turned out that I got 3 errors and they were happening at the the PetscInitialize(), and DACreate2d()<br>
<br>
line 79: PetscInitialize(&argc, &argv, (char*)0, help);<br>
line 84: ierr = DACreate2d(comm,DA_XPERIODIC,DA_STENCIL_BOX, -5, -5, PETSC_DECIDE, PETSC_DECIDE, 4, 2, 0, 0, &da);CHKERRQ(ierr);<br>
<br>
<br>
What could be wrong here? Thanks!<br>
<br>
The following is the message from valgrind<br>
<br>
-----------------------------------------------------------------<br>
valgrind --leak-check=full --show-reachable=yes --tool=memcheck ./vdthpffxmhd -options_file option_ffxmhd>output<br>
==26665== Memcheck, a memory error detector.<br>
==26665== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.<br>
==26665== Using LibVEX rev 1804, a library for dynamic binary translation.<br>
==26665== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.<br>
==26665== Using valgrind-3.3.0-Debian, a dynamic binary instrumentation framework.<br>
==26665== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.<br>
==26665== For more details, rerun with: -v<br>
==26665==<br>
==26665== Invalid read of size 4<br>
==26665== at 0x40151F9: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4005C59: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4007A87: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4011533: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4010F4D: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0291: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A29F: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429BEC5: __nss_hosts_lookup (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== Address 0x432af8c is 36 bytes inside a block of size 37 alloc'd<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x4008021: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4011533: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4010F4D: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0291: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A29F: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429BEC5: __nss_hosts_lookup (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x42A0782: gethostbyname_r (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665==<br>
==26665== Invalid read of size 4<br>
==26665== at 0x40151E3: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4005C59: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4007A87: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4011533: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4010F4D: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0291: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4731FFB: (within /lib/tls/i686/cmov/<a href="http://libnss_compat-2.7.so" target="_blank">libnss_compat-2.7.so</a>)<br>
==26665== by 0x473313C: _nss_compat_getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libnss_compat-2.7.so" target="_blank">libnss_compat-2.7.so</a>)<br>
==26665== Address 0x432c1f8 is 32 bytes inside a block of size 35 alloc'd<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x4008021: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4011533: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x4010F4D: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0291: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x400D5C5: (within /lib/<a href="http://ld-2.7.so" target="_blank">ld-2.7.so</a>)<br>
==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4731FFB: (within /lib/tls/i686/cmov/<a href="http://libnss_compat-2.7.so" target="_blank">libnss_compat-2.7.so</a>)<br>
==26665== by 0x473313C: _nss_compat_getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libnss_compat-2.7.so" target="_blank">libnss_compat-2.7.so</a>)<br>
==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665==<br>
==26665== ERROR SUMMARY: 3 errors from 2 contexts (suppressed: 41 from 1)<br>
==26665== malloc/free: in use at exit: 64,352 bytes in 87 blocks.<br>
==26665== malloc/free: 2,472 allocs, 2,385 frees, 3,015,115 bytes allocated.<br>
==26665== For counts of detected errors, rerun with: -v<br>
==26665== searching for pointers to 87 not-freed blocks.<br>
==26665== checked 1,120,136 bytes.<br>
==26665==<br>
==26665==<br>
==26665== 32 bytes in 2 blocks are still reachable in loss record 1 of 5<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x871B2A8: MPID_VCRT_Create (mpid_vc.c:62)<br>
==26665== by 0x8718C6A: MPID_Init (mpid_init.c:116)<br>
==26665== by 0x86F1C3B: MPIR_Init_thread (initthread.c:288)<br>
==26665== by 0x86F175D: PMPI_Init (init.c:106)<br>
==26665== by 0x86355A1: PetscInitialize (pinit.c:503)<br>
==26665== by 0x804B627: main (vdthpffxmhd.c:79)<br>
==26665==<br>
==26665==<br>
==26665== 156 (36 direct, 120 indirect) bytes in 1 blocks are definitely lost in loss record 2 of 5<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x429A3E2: (within /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x429AC2D: __nss_database_lookup (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4731FDB: ???<br>
==26665== by 0x473313C: ???<br>
==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x8644D41: PetscGetUserName (fuser.c:68)<br>
==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68)<br>
==26665== by 0x863565B: PetscInitialize (pinit.c:518)<br>
==26665== by 0x804B627: main (vdthpffxmhd.c:79)<br>
==26665==<br>
==26665==<br>
==26665== 40 bytes in 5 blocks are indirectly lost in loss record 3 of 5<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x4299FBB: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4731FFB: ???<br>
==26665== by 0x473313C: ???<br>
==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x8644D41: PetscGetUserName (fuser.c:68)<br>
==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68)<br>
==26665== by 0x863565B: PetscInitialize (pinit.c:518)<br>
==26665== by 0x804B627: main (vdthpffxmhd.c:79)<br>
==26665==<br>
==26665==<br>
==26665== 80 bytes in 5 blocks are indirectly lost in loss record 4 of 5<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x428739B: tsearch (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4299F7D: __nss_lookup_function (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x4731FFB: ???<br>
==26665== by 0x473313C: ???<br>
==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/<a href="http://libc-2.7.so" target="_blank">libc-2.7.so</a>)<br>
==26665== by 0x8644D41: PetscGetUserName (fuser.c:68)<br>
==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68)<br>
==26665== by 0x863565B: PetscInitialize (pinit.c:518)<br>
==26665== by 0x804B627: main (vdthpffxmhd.c:79)<br>
==26665==<br>
==26665==<br>
==26665== 64,164 bytes in 74 blocks are still reachable in loss record 5 of 5<br>
==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207)<br>
==26665== by 0x8610BE4: PetscMallocAlign (mal.c:40)<br>
==26665== by 0x8611CD3: PetscTrMallocDefault (mtr.c:194)<br>
==26665== by 0x81DE577: DACreate2d (da2.c:364)<br>
==26665== by 0x804B701: main (vdthpffxmhd.c:84)<br>
==26665==<br>
==26665== LEAK SUMMARY:<br>
==26665== definitely lost: 36 bytes in 1 blocks.<br>
==26665== indirectly lost: 120 bytes in 10 blocks.<br>
==26665== possibly lost: 0 bytes in 0 blocks.<br>
==26665== still reachable: 64,196 bytes in 76 blocks.<br>
==26665== suppressed: 0 bytes in 0 blocks.<br>
<br>
<br>
------------------------------------------------------------------<br><font color="#888888">
-- <br>
(Rebecca) Xuefei YUAN<br>
Department of Applied Physics and Applied Mathematics<br>
Columbia University<br>
Tel:917-399-8032<br>
<a href="http://www.columbia.edu/%7Exy2102" target="_blank">www.columbia.edu/~xy2102</a><br>
<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener<br>