Unable to pass all the tests with pnetcdf 1.6.1, Intel 15.0.3.048 and Mvapich2 2.1
Wei-keng Liao
wkliao at eecs.northwestern.edu
Tue Sep 22 16:10:13 CDT 2015
Hi, Craig
From these outputs, I think it is most likely due to MPI-IO fails
to return the same file striping unit and factor values among all
MPI processes. I guess only root process gets the correct values.
Attached is a short MPI program to test this theory.
Could you test it using at least 2 processes on Lustre?
To compile:
mpicc -o check_mpi_striping check_mpi_striping.c
To run:
mpiexec -n 2 check_mpi_striping
Wei-keng
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On Sep 22, 2015, at 2:34 PM, Craig Tierney - NOAA Affiliate wrote:
> Wei-keng,
>
> Here is the output from my run with PNETCDF_SAFE_MODE=1 on Lustre:
>
> [root at Jet:fe8 FLASH-IO]# mpiexec.hydra -env PNETCDF_SAFE_MODE 1 -np 4 ./flash_benchmark_io /lfs2/jetmgmt/Craig.Tierney/d1//flash_io_test_
> Warning (inconsistent metadata): variable lrefine's begin (root=1048576, local=3072)
> Warning (inconsistent metadata): variable nodetype's begin (root=2097152, local=4608)
> Warning (inconsistent metadata): variable gid's begin (root=3145728, local=6144)
> Warning (inconsistent metadata): variable coordinates's begin (root=4194304, local=25600)
> Warning (inconsistent metadata): variable blocksize's begin (root=5242880, local=33792)
> Warning (inconsistent metadata): variable bndbox's begin (root=6291456, local=41984)
> Warning (inconsistent metadata): variable dens's begin (root=7340032, local=57856)
> Warning (inconsistent metadata): variable velx's begin (root=18874368, local=10641920)
> Warning (inconsistent metadata): variable lrefine's begin (root=1048576, local=3072)
> Warning (inconsistent metadata): variable nodetype's begin (root=2097152, local=4608)
> Warning (inconsistent metadata): variable gid's begin (root=3145728, local=6144)
> Warning (inconsistent metadata): variable coordinates's begin (root=4194304, local=25600)
> Warning (inconsistent metadata): variable blocksize's begin (root=5242880, local=33792)
> Warning (inconsistent metadata): variable bndbox's begin (root=6291456, local=41984)
> Warning (inconsistent metadata): variable dens's begin (root=7340032, local=57856)
> Warning (inconsistent metadata): variable velx's begin (root=18874368, local=10641920)
> Warning (inconsistent metadata): variable vely's begin (root=30408704, local=21225984)
> Warning (inconsistent metadata): variable velz's begin (root=41943040, local=31810048)
> Warning (inconsistent metadata): variable pres's begin (root=53477376, local=42394112)
> Warning (inconsistent metadata): variable ener's begin (root=65011712, local=52978176)
> Warning (inconsistent metadata): variable temp's begin (root=76546048, local=63562240)
> Warning (inconsistent metadata): variable gamc's begin (root=88080384, local=74146304)
> Warning (inconsistent metadata): variable game's begin (root=99614720, local=84730368)
> Warning (inconsistent metadata): variable enuc's begin (root=111149056, local=95314432)
> Warning (inconsistent metadata): variable gpot's begin (root=122683392, local=105898496)
> Warning (inconsistent metadata): variable f1__'s begin (root=134217728, local=116482560)
> Warning (inconsistent metadata): variable f2__'s begin (root=145752064, local=127066624)
> Warning (inconsistent metadata): variable f3__'s begin (root=157286400, local=137650688)
> Warning (inconsistent metadata): variable lrefine's begin (root=1048576, local=3072)
> Warning (inconsistent metadata): variable nodetype's begin (root=2097152, local=4608)
> Warning (inconsistent metadata): variable gid's begin (root=3145728, local=6144)
> Warning (inconsistent metadata): variable coordinates's begin (root=4194304, local=25600)
> Warning (inconsistent metadata): variable blocksize's begin (root=5242880, local=33792)
> Warning (inconsistent metadata): variable bndbox's begin (root=6291456, local=41984)
> Warning (inconsistent metadata): variable dens's begin (root=7340032, local=57856)
> Warning (inconsistent metadata): variable velx's begin (root=18874368, local=10641920)
> Warning (inconsistent metadata): variable vely's begin (root=30408704, local=21225984)
> Warning (inconsistent metadata): variable velz's begin (root=41943040, local=31810048)
> Warning (inconsistent metadata): variable pres's begin (root=53477376, local=42394112)
> Warning (inconsistent metadata): variable ener's begin (root=65011712, local=52978176)
> Warning (inconsistent metadata): variable temp's begin (root=76546048, local=63562240)
> Warning (inconsistent metadata): variable gamc's begin (root=88080384, local=74146304)
> Warning (inconsistent metadata): variable game's begin (root=99614720, local=84730368)
> Warning (inconsistent metadata): variable enuc's begin (root=111149056, local=95314432)
> Warning (inconsistent metadata): variable gpot's begin (root=122683392, local=105898496)
> Warning (inconsistent metadata): variable f1__'s begin (root=134217728, local=116482560)
> Warning (inconsistent metadata): variable f2__'s begin (root=145752064, local=127066624)
> Warning (inconsistent metadata): variable f3__'s begin (root=157286400, local=137650688)
> Warning (inconsistent metadata): variable f4__'s begin (root=168820736, local=148234752)
> Warning (inconsistent metadata): variable f5__'s begin (root=180355072, local=158818816)
> Warning (inconsistent metadata): variable f6__'s begin (root=191889408, local=169402880)
> Warning (inconsistent metadata): variable vely's begin (root=30408704, local=21225984)
> Warning (inconsistent metadata): variable velz's begin (root=41943040, local=31810048)
> Warning (inconsistent metadata): variable pres's begin (root=53477376, local=42394112)
> Warning (inconsistent metadata): variable ener's begin (root=65011712, local=52978176)
> Warning (inconsistent metadata): variable temp's begin (root=76546048, local=63562240)
> Warning (inconsistent metadata): variable gamc's begin (root=88080384, local=74146304)
> Warning (inconsistent metadata): variable game's begin (root=99614720, local=84730368)
> Warning (inconsistent metadata): variable enuc's begin (root=111149056, local=95314432)
> Warning (inconsistent metadata): variable gpot's begin (root=122683392, local=105898496)
> Warning (inconsistent metadata): variable f1__'s begin (root=134217728, local=116482560)
> Warning (inconsistent metadata): variable f2__'s begin (root=145752064, local=127066624)
> Warning (inconsistent metadata): variable f3__'s begin (root=157286400, local=137650688)
> Warning (inconsistent metadata): variable f4__'s begin (root=168820736, local=148234752)
> Warning (inconsistent metadata): variable f5__'s begin (root=180355072, local=158818816)
> Warning (inconsistent metadata): variable f6__'s begin (root=191889408, local=169402880)
> Warning (inconsistent metadata): variable f7__'s begin (root=203423744, local=179986944)
> Warning (inconsistent metadata): variable f8__'s begin (root=214958080, local=190571008)
> Warning (inconsistent metadata): variable f9__'s begin (root=226492416, local=201155072)
> Warning (inconsistent metadata): variable f10_'s begin (root=238026752, local=211739136)
> Warning (inconsistent metadata): variable f11_'s begin (root=249561088, local=222323200)
> Warning (inconsistent metadata): variable f12_'s begin (root=261095424, local=232907264)
> Warning (inconsistent metadata): variable f13_'s begin (root=272629760, local=243491328)
> Warning (inconsistent metadata): variable f4__'s begin (root=168820736, local=148234752)
> Warning (inconsistent metadata): variable f5__'s begin (root=180355072, local=158818816)
> Warning (inconsistent metadata): variable f6__'s begin (root=191889408, local=169402880)
> Warning (inconsistent metadata): variable f7__'s begin (root=203423744, local=179986944)
> Warning (inconsistent metadata): variable f8__'s begin (root=214958080, local=190571008)
> Warning (inconsistent metadata): variable f9__'s begin (root=226492416, local=201155072)
> Warning (inconsistent metadata): variable f10_'s begin (root=238026752, local=211739136)
> Warning (inconsistent metadata): variable f11_'s begin (root=249561088, local=222323200)
> Warning (inconsistent metadata): variable f12_'s begin (root=261095424, local=232907264)
> Warning (inconsistent metadata): variable f13_'s begin (root=272629760, local=243491328)
> Warning (inconsistent metadata): variable f7__'s begin (root=203423744, local=179986944)
> Warning (inconsistent metadata): variable f8__'s begin (root=214958080, local=190571008)
> Warning (inconsistent metadata): variable f9__'s begin (root=226492416, local=201155072)
> Warning (inconsistent metadata): variable f10_'s begin (root=238026752, local=211739136)
> Warning (inconsistent metadata): variable f11_'s begin (root=249561088, local=222323200)
> Warning (inconsistent metadata): variable f12_'s begin (root=261095424, local=232907264)
> Warning (inconsistent metadata): variable f13_'s begin (root=272629760, local=243491328)
> Here: -250
> Here: -262
> Here: -262
> Here: -262
> nfmpi_enddefFile header is inconsistent among processes
> nfmpi_enddef
> (Internal error) beginning file offset of this variable is inconsistent among p
> r
> nfmpi_enddef
> (Internal error) beginning file offset of this variable is inconsistent among p
> r
> nfmpi_enddef
> (Internal error) beginning file offset of this variable is inconsistent among p
> r
> [cli_1]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
> [cli_0]: [cli_2]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
> [cli_3]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
> aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>
> Craig
>
> On Mon, Sep 21, 2015 at 1:21 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
>
> It is strange that the test failed for Lustre.
>
> The error message says some variables defined across MPI processes are not consistent.
> Could you run this benchmark with safe mode on? by setting the environment variable
> PNETCDF_SAFE_MODE to 1 before the run. This will print more error messages, such as
> which variables are inconsistent and at what offsets.
>
>
> Wei-keng
>
> On Sep 21, 2015, at 1:31 PM, Craig Tierney - NOAA Affiliate wrote:
>
> > Rob and Wei-keng,
> >
> > Thanks for you help on this problem. Rob - The patch seems to work. I had to hand apply it but now the pnetcdf tests (mostly) complete successfully. The FLASH-IO benchmark is failing when Lustre is used. It completes successfully when Panasas is used. The error code that is returned by nfmpi_enddef is -262. The description for this error is:
> >
> > #define NC_EMULTIDEFINE_VAR_BEGIN (-262) /**< inconsistent variable file begin offset (internal use) */
> >
> > [root at Jet:fe7 FLASH-IO]# mpiexec.hydra -n 4 ./flash_benchmark_io /pan2/jetmgmt/Craig.Tierney/pan_flash_io_test_
> > Here: 0
> > Here: 0
> > Here: 0
> > Here: 0
> > number of guards : 4
> > number of blocks : 80
> > number of variables : 24
> > checkpoint time : 12.74 sec
> > max header : 0.88 sec
> > max unknown : 11.83 sec
> > max close : 0.53 sec
> > I/O amount : 242.30 MiB
> > plot no corner : 2.38 sec
> > max header : 0.59 sec
> > max unknown : 1.78 sec
> > max close : 0.22 sec
> > I/O amount : 20.22 MiB
> > plot corner : 2.52 sec
> > max header : 0.81 sec
> > max unknown : 1.51 sec
> > max close : 0.96 sec
> > I/O amount : 24.25 MiB
> > -------------------------------------------------------
> > File base name : /pan2/jetmgmt/Craig.Tierney/pan_flash_io_test_
> > file striping count : 0
> > file striping size : 301346992 bytes
> > Total I/O amount : 286.78 MiB
> > -------------------------------------------------------
> > nproc array size exec (sec) bandwidth (MiB/s)
> > 4 16 x 16 x 16 17.64 16.26
> >
> >
> > [root at Jet:fe7 FLASH-IO]# mpiexec.hydra -n 4 ./flash_benchmark_io /lfs2/jetmgmt/Craig.Tierney/lfs_flash_io_test_
> > Here: -262
> > Here: -262
> > Here: -262
> > nfmpi_enddef
> > (Internal error) beginning file offset of this variable is inconsistent among p
> > r
> > nfmpi_enddef
> > (Internal error) beginning file offset of this variable is inconsistent among p
> > r
> > nfmpi_enddef
> > (Internal error) beginning file offset of this variable is inconsistent among p
> > r
> > Here: 0
> > [cli_1]: aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
> > [cli_3]: [cli_2]: aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
> > aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
> >
> > ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = PID 16702 RUNNING AT fe7
> > = EXIT CODE: 255
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> > ===================================================================================
> >
> > Thanks,
> > Craig
> >
> >
> > On Mon, Sep 21, 2015 at 8:30 AM, Rob Latham <robl at mcs.anl.gov> wrote:
> >
> >
> > On 09/20/2015 03:44 PM, Craig Tierney - NOAA Affiliate wrote:
> > Wei-keng,
> >
> > I tried your test code on a different system, and I found it worked with
> > Intel+mvapich2 (2.1rc1). That system was using Panasas and I was
> > testing on Lustre. I then tried Panasas on the original machine
> > (supports both Panasas and Lustre) and I got the correct behavior.
> >
> > So the problem somehow related to Lustre. We are using the 2.5.37.ddn
> > client. Unless you have an obvious answer, I will open this with DDN
> > tomorrow.
> >
> >
> > Ah, bet I know why this is!
> >
> > the Lustre driver and (some versions of the) Panasas driver set their fs-specific hints by opening the file, setting some ioctls, then continuing on without deleting the file.
> >
> > In the common case, when we expect the file to show up, no one notices or cares, but in MPI_MODE_EXCL or some other restrictive flags, the file gets created when we did not expect it to -- and that's part of the reason this bug lived on so long.
> >
> > I fixed this by moving file manipulations out of the hint parsing path and into the open path (after we check permissions and flags)
> >
> > Relevant commit: https://trac.mpich.org/projects/mpich/changeset/92f1c69f0de87f9
> >
> > See more details from Darshan, OpenMPI, and MPICH here:
> > - https://trac.mpich.org/projects/mpich/ticket/2261
> > - https://github.com/open-mpi/ompi/issues/158
> > - http://lists.mcs.anl.gov/pipermail/darshan-users/2015-February/000256.html
> >
> > ==rob
> >
> >
> > Thanks,
> > Craig
> >
> > On Sun, Sep 20, 2015 at 2:36 PM, Craig Tierney - NOAA Affiliate
> > <craig.tierney at noaa.gov <mailto:craig.tierney at noaa.gov>> wrote:
> >
> > Wei-keng,
> >
> > Thanks for the test case. Here is what I get using a set of
> > compilers and MPI stacks. I was expecting that mvapich2 1.8 and 2.1
> > would behave differently.
> >
> > What versions of MPI do you test internally?
> >
> > Craig
> >
> > Testing intel+impi
> >
> > Currently Loaded Modules:
> > 1) newdefaults 2) intel/15.0.3.187 <http://15.0.3.187> 3)
> > impi/5.1.1.109 <http://5.1.1.109>
> >
> > Error at line 22: File does not exist, error stack:
> > ADIOI_NFS_OPEN(69): File /lfs3/jetmgmt/Craig.Tierney/tooth-fairy.nc
> > <http://tooth-fairy.nc> does not exist
> > Testing intel+mvapich2 2.1
> >
> > Currently Loaded Modules:
> > 1) newdefaults 2) intel/15.0.3.187 <http://15.0.3.187> 3)
> > mvapich2/2.1
> >
> > file was opened: /lfs3/jetmgmt/Craig.Tierney/tooth-fairy.nc
> > <http://tooth-fairy.nc>
> > Testing intel+mvapich2 1.8
> >
> > Currently Loaded Modules:
> > 1) newdefaults 2) intel/15.0.3.187 <http://15.0.3.187> 3)
> > mvapich2/1.8
> >
> > file was opened: /lfs3/jetmgmt/Craig.Tierney/tooth-fairy.nc
> > <http://tooth-fairy.nc>
> > Testing pgi+mvapich2 2.1
> >
> > Currently Loaded Modules:
> > 1) newdefaults 2) pgi/15.3 3) mvapich2/2.1
> >
> > file was opened: /lfs3/jetmgmt/Craig.Tierney/tooth-fairy.nc
> > <http://tooth-fairy.nc>
> > Testing pgi+mvapich2 1.8
> >
> > Currently Loaded Modules:
> > 1) newdefaults 2) pgi/15.3 3) mvapich2/1.8
> >
> > file was opened: /lfs3/jetmgmt/Craig.Tierney/tooth-fairy.nc
> > <http://tooth-fairy.nc>
> >
> > Craig
> >
> > On Sun, Sep 20, 2015 at 1:43 PM, Wei-keng Liao
> > <wkliao at eecs.northwestern.edu <mailto:wkliao at eecs.northwestern.edu>>
> > wrote:
> >
> > In that case, it is likely mvapich does not perform correctly.
> >
> > In PnetCDF, when NC_NOWRITE is used in a call to ncmpi_open,
> > PnetCDF calls a MPI_File_open with the open flag set to
> > MPI_MODE_RDONLY. See
> > http://trac.mcs.anl.gov/projects/parallel-netcdf/browser/tags/v1-6-1/src/lib/mpincio.c#L322
> >
> > Maybe test this with a simple MPI-IO program below.
> > It prints error messages like
> > Error at line 15: File does not exist, error stack:
> > ADIOI_UFS_OPEN(69): File tooth-fairy.nc
> > <http://tooth-fairy.nc> does not exist
> >
> > But, no file should be created.
> >
> >
> > #include <stdio.h>
> > #include <unistd.h> /* unlink() */
> > #include <mpi.h>
> >
> > int main(int argc, char **argv) {
> > int err;
> > MPI_File fh;
> >
> > MPI_Init(&argc, &argv);
> >
> > /* delete "tooth-fairy.nc <http://tooth-fairy.nc>" and
> > ignore the error */
> > unlink("tooth-fairy.nc <http://tooth-fairy.nc>");
> >
> > err = MPI_File_open(MPI_COMM_WORLD, "tooth-fairy.nc
> > <http://tooth-fairy.nc>", MPI_MODE_RDONLY, MPI_INFO_NULL, &fh);
> > if (err != MPI_SUCCESS) {
> > int errorStringLen;
> > char errorString[MPI_MAX_ERROR_STRING];
> > MPI_Error_string(err, errorString, &errorStringLen);
> > printf("Error at line %d: %s\n",__LINE__, errorString);
> > }
> > else
> > MPI_File_close(&fh);
> >
> > MPI_Finalize();
> > return 0;
> > }
> >
> >
> > Wei-keng
> >
> > On Sep 20, 2015, at 1:51 PM, Craig Tierney - NOAA Affiliate wrote:
> >
> > > Wei-keng,
> > >
> > > I always run distclean before I try to build the code. The
> > first test failing is nc_test. The problem seems to be in this
> > test:
> > >
> > > err = ncmpi_open(comm, "tooth-fairy.nc
> > <http://tooth-fairy.nc>", NC_NOWRITE, info, &ncid);/* should fail */
> > > IF (err == NC_NOERR)
> > > error("ncmpi_open of nonexistent file should have
> > failed");
> > > IF (err != NC_ENOENT)
> > > error("ncmpi_open of nonexistent file should have
> > returned NC_ENOENT");
> > > else {
> > > /* printf("Expected error message complaining: \"File
> > tooth-fairy.nc <http://tooth-fairy.nc> does not exist\"\n"); */
> > > nok++;
> > > }
> > >
> > > A zero length tooth-fairy.nc <http://tooth-fairy.nc> file is
> > being created, and I don't think that is supposed to happen.
> > That would mean that the mode NC_NOWRITE is not being honored by
> > MPI_IO. I will look at this more tomorrow and try to craft a
> > short example.
> > >
> > > Craig
> > >
> > > On Sun, Sep 20, 2015 at 10:23 AM, Wei-keng Liao
> > <wkliao at eecs.northwestern.edu
> > <mailto:wkliao at eecs.northwestern.edu>> wrote:
> > > Hi, Craig
> > >
> > > Your config.log looks fine to me.
> > > Some of your error messages are supposed to report errors of
> > opening
> > > a non-existing file, but report a different error code,
> > meaning the
> > > file does exist. I suspect it may be because of residue files.
> > >
> > > Could you do a clean rebuild with the following commands?
> > > % make -s distclean
> > > % ./configure --prefix=/apps/pnetcdf/1.6.1-intel-mvapich2
> > > % make -s -j8
> > > % make -s check
> > >
> > > If the problem persists, then it might be because mvapich.
> > >
> > > Wei-keng
> > >
> >
> >
> >
> >
> > --
> > Rob Latham
> > Mathematics and Computer Science Division
> > Argonne National Lab, IL USA
> >
>
>
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