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POOpenMPI debugging with Valgrind and suppressions in OS X
 

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  1. POOpenMPI debugging with Valgrind and suppressions in OS X
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    <p>I am writing a parallel code in C++ on my OS X (Snow Leopard) laptop, and I am trying to debug it with memchecker. I have successfully built OpenMPI with valgrind support with: <code>configure --prefix=/opt/openmpi-1.4.3/ --enable-debug --enable-memchecker --with-valgrind=/opt/valgrind-3.6.0/ FFLAGS=-m64 F90FLAGS=-m64</code> (Ignore the Fortran flags, it's due to my Fortran compiler being from GCC).</p> <p>When I run my application with</p> <blockquote> <p>mpirun -np 2 valgrind --suppressions=/opt/openmpi-1.4.3/share/openmpi/openmpi-valgrind.supp --leak-check=yes --dsymutil=yes ./program</p> </blockquote> <p>I get a whole lot of warnings from Valgrind (the most of them from the heap summary at the end). I have included a small snippet of the warnings below. What I get from them is that Valgrind detects memory leaks and uninitialised values in the MPI library, but I'm not really interested in that. I want warnings from the code I write. I already run Valgrind with the suppression file provided by OpenMPI, but evidently it is not enough. How can I easily ignore all the other warnings detected in the OpenMPI distribution? Is it possible to find a suppression file for OpenMPI debugging with Valgrind on OS X, or do you know any cunning trick?</p> <p>The first warning is</p> <pre><code> ==1531== Syscall param writev(vector[...]) points to uninitialised byte(s) ==1531== at 0x1014E16E2: writev (in /usr/lib/libSystem.B.dylib) ==1531== by 0x101AEA4C5: mca_oob_tcp_peer_send (in /opt/openmpi-1.4.3/lib/openmpi/mca_oob_tcp.so) ==1531== by 0x101AF0B88: mca_oob_tcp_send_nb (in /opt/openmpi-1.4.3/lib/openmpi/mca_oob_tcp.so) ==1531== by 0x101AC7F48: orte_rml_oob_send (in /opt/openmpi-1.4.3/lib/openmpi/mca_rml_oob.so) ==1531== by 0x101AC8AA1: orte_rml_oob_send_buffer (in /opt/openmpi-1.4.3/lib/openmpi/mca_rml_oob.so) ==1531== by 0x101B3489E: allgather (in /opt/openmpi-1.4.3/lib/openmpi/mca_grpcomm_bad.so) ==1531== by 0x101B3525D: modex (in /opt/openmpi-1.4.3/lib/openmpi/mca_grpcomm_bad.so) ==1531== by 0x1000A48E6: ompi_mpi_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000F7806: MPI_Init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100001AF2: main (main.cpp:34) ==1531== Address 0x101a8911b is 107 bytes inside a block of size 256 alloc'd ==1531== at 0x10002DB2D: realloc (vg_replace_malloc.c:525) ==1531== by 0x1012240B6: opal_dss_buffer_extend (in /opt/openmpi-1.4.3/lib/libopen- pal.0.dylib) ==1531== by 0x101225CF7: opal_dss_copy_payload (in /opt/openmpi-1.4.3/lib/libopen-pal.0.dylib) ==1531== by 0x101B347CA: allgather (in /opt/openmpi-1.4.3/lib/openmpi/mca_grpcomm_bad.so) ==1531== by 0x101B3525D: modex (in /opt/openmpi-1.4.3/lib/openmpi/mca_grpcomm_bad.so) ==1531== by 0x1000A48E6: ompi_mpi_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000F7806: MPI_Init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100001AF2: main (main.cpp:34) </code></pre> <p>After execution a small snippet of the heap summary looks like this</p> <pre><code> ==1531== 88 bytes in 1 blocks are definitely lost in loss record 1,950 of 2,194 ==1531== at 0x10002D915: malloc (vg_replace_malloc.c:236) ==1531== by 0x100073888: opal_obj_new (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073808: opal_obj_new_debug (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073C17: ompi_attr_create_keyval_impl (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073FCF: ompi_attr_create_keyval (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100077C96: create_comm (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x10007798A: ompi_attr_create_predefined (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000737CF: ompi_attr_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000A4840: ompi_mpi_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000F7806: MPI_Init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100001AF2: main (main.cpp:34) </code></pre> <blockquote> <p>...</p> </blockquote> <pre><code> ==1531== 88 bytes in 1 blocks are definitely lost in loss record 1,952 of 2,194 ==1531== at 0x10002D915: malloc (vg_replace_malloc.c:236) ==1531== by 0x100073888: opal_obj_new (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073808: opal_obj_new_debug (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073C17: ompi_attr_create_keyval_impl (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073FCF: ompi_attr_create_keyval (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x10014CEC5: PMPI_Keyval_create (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1065ACFE6: ??? ==1531== by 0x10658867B: ??? ==1531== by 0x10017A591: module_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100179985: mca_io_base_file_select (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100089D55: ompi_file_open (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1000E1ED1: MPI_File_open (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== ==1531== 88 bytes in 1 blocks are definitely lost in loss record 1,953 of 2,194 ==1531== at 0x10002D915: malloc (vg_replace_malloc.c:236) ==1531== by 0x100073888: opal_obj_new (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073808: opal_obj_new_debug (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073C17: ompi_attr_create_keyval_impl (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x100073FCF: ompi_attr_create_keyval (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x10014CEC5: PMPI_Keyval_create (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) ==1531== by 0x1065A6210: ??? ==1531== by 0x106597149: ??? ==1531== by 0x106596AAB: ??? ==1531== by 0x1065AD14C: ??? ==1531== by 0x10658867B: ??? ==1531== by 0x10017A591: module_init (in /opt/openmpi-1.4.3/lib/libmpi.0.dylib) </code></pre>
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    1. COJust to be clarify: I don't know if this is an OS X issue or the same on Linux systems as I haven't tested it on a Linux system.
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    2. COto format code samples or program output, please, don't use `>` symbol. Select the code sample and press button "{}" at top panel. It will add 4 space symbols (0x20) at beggining of every line
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