[mpich-discuss] Potentially odd memory behavior in MPI_Waitall

John Grime jgrime at uchicago.edu
Sat Jan 4 11:58:09 CST 2014


Hi Ken,

I tried again to create a minimal demonstration, and I think I now have such an example. Code attached.


Notes:

- Each MPI rank creates its own log file to print results to, for easy examination of data from the different processes.

- The “BufferExchange” object is designed for easy sharing of arbitrary data buffers between a specified set of peer ranks.

- I added memory check code around various aspects of the buffer exchanges ( see BufferExchange::FullExchange() ), and I print the memory changes at the end of each FullExchange() call (these are in KB on OSX).

- The most interesting value is “final_waitall”, the measured resident set memory increase due to calling the final MPI_Waitall() ( see BufferExchange::FullExchange() ).

- I tested both fixed-size buffers, and variable-sized buffers (either 100 integers per buffer, or buffers of the same size as the loop iteration number)

- The memory increases seem to be nondeterministic: running the same program several times gives me different values. I think this might suggest it’s due to the OS.


I built and ran the example using:

mpicxx -Wall -Wextra base.cpp BufferExchange.cpp main.cpp

mpiexec -np 4 ./a.out

… and the output files were therefore “log.0” to “log.3”.

Apologies for any obvious bugs in the code
, it was something of a rush job.

Cheers,

J.


On Jan 2, 2014, at 9:53 PM, Kenneth Raffenetti <raffenet at mcs.anl.gov> wrote:

> Can you provide a minimal demonstration of this behavior? That way we can work from the same reference point to identify possible causes.
>
> On 01/01/2014 03:05 PM, John Grime wrote:
>> Hi all,
>>
>> I was wondering if someone could help me out with trying to understand what’s gong on with an MPI_Waitall() call with regards to resident set memory usage. Platform information at the end of the email.
>>
>> If I run a 4 process MPI job on my desktop machine, I get a steady increase in memory usage over the course of the program. Apart from the places where I would reasonably expect expect memory usage to increase, I also see regular increases when I call MPI_Waitall().
>>
>> I measure this behavior via:
>>
>> getmem( &rss0, &vs );
>>
>> result = MPI_Waitall( n_buffer_reqs, buffer_reqs, MPI_STATUSES_IGNORE );
>> if( result != MPI_SUCCESS ) ERROR_MACRO( "MPI_Waitall" );
>>
>> getmem( &rss1, &vs );
>>
>> … where getmem() queries the OS kernel to return the resident set size (“rss") and virtual memory size (“vs", ignored). The getmem() function does not allocate any memory itself, so I can hopefully see any difference in the resident set memory used before and after the MPI_Waitall() call via (rss1-rss0).
>>
>> After MPI_Waitall() returns, I very often see an increase in the resident set size ranging from 4096 bytes to 65536 bytes.
>>
>> Running an “identical” 4-process job on a single node of the Blue Waters compute cluster (Cray XE system, GCC 4.8.1, Cray mpich 6.0.1) does not seem to produce this behaviour.
>>
>> Switching the MPI_Waitall() for a loop over MPI_Waitany() calls also produces resident set increases.
>>
>> Does anyone have any comments or suggestions as to how I might understand whether this behavior is errant, and how I might track down the cause? It’s irritating me as I’d really like to produce code with as low a memory overhead as possible!
>>
>> Cheers,
>>
>> J.
>>
>> ------------------
>> Platform info:
>> ------------------
>>
>> OS: Apple OSX 10.9.1
>>
>> mpicxx —version:
>>
>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>> Target: x86_64-apple-darwin13.0.0
>> Thread model: posix
>>
>> mpiexec —version
>>
>> HYDRA build details:
>>     Version:                                 3.0.4
>>     Release Date:                            Wed Apr 24 10:08:10 CDT 2013
>>     CC:                              /usr/bin/clang  -pipe -arch x86_64 -Wl,-headerpad_max_install_names -arch x86_64
>>     CXX:                             /usr/bin/clang++  -pipe -arch x86_64 -Wl,-headerpad_max_install_names -arch x86_64
>>     F77:                             /opt/local/bin/gfortran-mp-4.8 -pipe -m64 -Wl,-headerpad_max_install_names -arch x86_64
>>     F90:                             /opt/local/bin/gfortran-mp-4.8 -pipe -m64 -Wl,-headerpad_max_install_names -arch x86_64
>>     Configure options:                       '--disable-option-checking' '--prefix=/opt/local' '--disable-dependency-tracking' '--disable-silent-rules' '--enable-base-cache' '--enable-cache' '--enable-cxx' '--enable-fast=O2' '--enable-shared' '--enable-smpcoll' '--with-device=ch3:nemesis' '--with-pm=hydra' '--with-thread-package=posix' '--enable-versioning' 'F90FLAGS=' 'F90=' '--enable-timer-type=mach_absolute_time' '--libdir=/opt/local/lib/mpich-mp' '--sysconfdir=/opt/local/etc/mpich-mp' '--program-suffix=-mp' '--enable-f77' '--enable-fc' 'CC=/usr/bin/clang' 'CFLAGS=-pipe -arch x86_64 -O2' 'LDFLAGS=-Wl,-headerpad_max_install_names -arch x86_64 ' 'CXX=/usr/bin/clang++' 'CXXFLAGS=-pipe -arch x86_64 -O2' 'F77=/opt/local/bin/gfortran-mp-4.8' 'FFLAGS=-pipe -m64 -O2' 'FC=/opt/local/bin/gfortran-mp-4.8' 'FCFLAGS=-pipe -m64 -O2' '--cache-file=/dev/null' '--srcdir=.' 'LIBS=-lpthread ' 'CPPFLAGS= -I/opt/local/var/macports/build/_opt_mports_dports_science_mpich/mpich-default/work/mpich-3.0.4
> /src/mpl/include -I/opt/local/var/macports/build/_opt_mports_dports_science_mpich/mpich-default/work/mpich-3.0.4/src/mpl/include -I/opt/local/var/macports/build/_opt_mports_dports_science_mpich/mpich-default/work/mpich-3.0.4/src/openpa/src -I/opt/local/var/macports/build/_opt_mports_dports_science_mpich/mpich-default/work/mpich-3.0.4/src/openpa/src -I/opt/local/var/macports/build/_opt_mports_dports_science_mpich/mpich-default/work/mpich-3.0.4/src/mpi/romio/include'
>>     Process Manager:                         pmi
>>     Launchers available:                     ssh rsh fork slurm ll lsf sge manual persist
>>     Topology libraries available:            hwloc
>>     Resource management kernels available:   user slurm ll lsf sge pbs cobalt
>>     Checkpointing libraries available:
>>     Demux engines available:                 poll select
>>
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