[petsc-dev] petsc-3.13.2.tar.gz now available

2020-06-02 Thread Satish Balay via petsc-dev 
Dear PETSc users,

The patch release petsc-3.13.2 is now available for download,
with change list at 'PETSc-3.13 Changelog'

http://www.mcs.anl.gov/petsc/download/index.html

Satish

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Jed Brown 
Jacob Faibussowitsch  writes:

> 2. (More a question for Jed) If I am using Jeds docker image anyways and we 
> have CI/CD builds also using his docker images (correct me if I am wrong 
> here) and a valgrind build in stage 3 why not include those build arguments 
> in the MPICH included in the images? I think the valgrind build for CI/CD 
> actually downloads and builds MPICH through petsc configure, is this because 
> of the errors I detailed below?

I'd welcome a PR to add options like --enable-g=meminit.  I'd rather not
make that general-purpose image use ch3:sock because people also use it
(via Singularity or Shifter) for performance.  We could make a different
Docker image with ch3:sock.

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Satish Balay via petsc-dev 
If using docker - I would think you should be able to make changes [as you 
need] and save them [as your own docker image file].

And wrt PETSC-CI, only stage-1 tests use the docker images.

A single image for the whole CI doesn't make any sense. [we test different 
OSes, different compilers, different variants of linux, different configure 
features - i.e use pre-installed packages, also test configure features to 
install install packages etc].

And yes - valgrind build in CI uses --download-mpich [ andno docker here - its 
one of the slowest builds - so needs to be run on the fastest machine we have 
access to]

Satish

On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:

> > MPICH need to be built with the option --enable-g=meminit for it to be 
> > valgrind clean.
> I see. Two questions:
> 
> 1. I am using Jeds docker image for MPICH (actually this is the main reason 
> for using Jeds image, as configuring and building MPICH takes an absolute age 
> on docker), will this re-build the MPICH already installed in the image or 
> download and build an entirely new MPICH?
> 
> 2. (More a question for Jed) If I am using Jeds docker image anyways and we 
> have CI/CD builds also using his docker images (correct me if I am wrong 
> here) and a valgrind build in stage 3 why not include those build arguments 
> in the MPICH included in the images? I think the valgrind build for CI/CD 
> actually downloads and builds MPICH through petsc configure, is this because 
> of the errors I detailed below?
> 
> Best regards,
> 
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
> Cell: (312) 694-3391
> 
> > On Jun 2, 2020, at 11:59 AM, Satish Balay  wrote:
> > 
> > MPICH need to be built with the option --enable-g=meminit for it to be 
> > valgrind clean.
> > 
> > --download-mpich does this [among other things that are useful during 
> > software developement]. Pre-configured MPICH is not likely to do this.
> > 
> > You can verify with: mpichversion
> > 
> > You can prebuild MPICH using PETSc with:
> > 
> > ./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS= 
> > CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=
> > 
> > And make this your default pre-installed MPI. [by adding $HOME/soft/mpich 
> > to PATH]
> > 
> > Satish
> > 
> > 
> > On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:
> > 
> >> Yes I am using the pre-loaded MPICH from the docker image. Further proof 
> >> from configure
> >> 
> >> #define PETSC_HAVE_MPICH_NUMVERSION 30302300
> >> #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
> >> 
> >> Best regards,
> >> 
> >> Jacob Faibussowitsch
> >> (Jacob Fai - booss - oh - vitch)
> >> Cell: (312) 694-3391
> >> 
> >>> On Jun 2, 2020, at 11:35 AM, Junchao Zhang  
> >>> wrote:
> >>> 
> >>> I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() 
> >>> is from MPICH. 
> >>> 
> >>> --Junchao Zhang
> >>> 
> >>> 
> >>> On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev 
> >>> mailto:petsc-dev@mcs.anl.gov> 
> >>> >> wrote:
> >>> use --download-mpich for valgrind.
> >>> 
> >>> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
> >>>  >>>  >
> >>> 
> >>> Satish
> >>> 
> >>> On Tue, 2 Jun 2020, Karl Rupp wrote:
> >>> 
>  Hi Jacob,
>  
>  the recommendation in the past was to use MPICH as it is (was?)
>  valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
>  issues. (My information might be outdated)
>  
>  Best regards,
>  Karli
>  
>  On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > Hello All,
> > 
> > TL;DR: valgrind always complains about "Syscall param write(buf) points 
> > to
> > uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> > debugging using valgrind fairly annoying since I have to sort through a 
> > ton
> > of unrelated stuff. I have built valgrind from source, used apt install
> > valgrind, apt install valgrind-mpi to no avail.
> > 
> > I am using valgrind from docker. Dockerfile is attached below as well. I
> > have been unsuccessfully trying to resolve these local valgrind errors, 
> > but
> > I am running out of ideas. Googling the issue has also not provided 
> > entirely
> > applicable solutions. Here is an example of the error:
> > 
> > $ make -f gmakefile test VALGRIND=1
> > ...
> > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > #==54610==at 0x6F63317: write (write.c:26)
> > #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Jacob Faibussowitsch 
> You can verify with: mpichversion
Yes you’re right. Here is what this produces for me

MPICH Version:  3.3.2
MPICH Release date: Tue Nov 12 21:23:16 CST 2019
MPICH Device:   ch3:sock
MPICH configure:--disable-wrapper-rpath --with-device=ch3:sock
MPICH CC:   gcc-O2
MPICH CXX:  g++   -O2
MPICH F77:  gfortran   -O2
MPICH FC:   gfortran   -O2
MPICH Custom Information:   

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391

> On Jun 2, 2020, at 11:59 AM, Satish Balay  wrote:
> 
> MPICH need to be built with the option --enable-g=meminit for it to be 
> valgrind clean.
> 
> --download-mpich does this [among other things that are useful during 
> software developement]. Pre-configured MPICH is not likely to do this.
> 
> You can verify with: mpichversion
> 
> You can prebuild MPICH using PETSc with:
> 
> ./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS= 
> CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=
> 
> And make this your default pre-installed MPI. [by adding $HOME/soft/mpich to 
> PATH]
> 
> Satish
> 
> 
> On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:
> 
>> Yes I am using the pre-loaded MPICH from the docker image. Further proof 
>> from configure
>> 
>> #define PETSC_HAVE_MPICH_NUMVERSION 30302300
>> #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
>> 
>> Best regards,
>> 
>> Jacob Faibussowitsch
>> (Jacob Fai - booss - oh - vitch)
>> Cell: (312) 694-3391
>> 
>>> On Jun 2, 2020, at 11:35 AM, Junchao Zhang  wrote:
>>> 
>>> I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() is 
>>> from MPICH. 
>>> 
>>> --Junchao Zhang
>>> 
>>> 
>>> On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev 
>>> mailto:petsc-dev@mcs.anl.gov> 
>>> >> wrote:
>>> use --download-mpich for valgrind.
>>> 
>>> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
>>> >>  >
>>> 
>>> Satish
>>> 
>>> On Tue, 2 Jun 2020, Karl Rupp wrote:
>>> 
 Hi Jacob,
 
 the recommendation in the past was to use MPICH as it is (was?)
 valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
 issues. (My information might be outdated)
 
 Best regards,
 Karli
 
 On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> Hello All,
> 
> TL;DR: valgrind always complains about "Syscall param write(buf) points to
> uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> debugging using valgrind fairly annoying since I have to sort through a 
> ton
> of unrelated stuff. I have built valgrind from source, used apt install
> valgrind, apt install valgrind-mpi to no avail.
> 
> I am using valgrind from docker. Dockerfile is attached below as well. I
> have been unsuccessfully trying to resolve these local valgrind errors, 
> but
> I am running out of ideas. Googling the issue has also not provided 
> entirely
> applicable solutions. Here is an example of the error:
> 
> $ make -f gmakefile test VALGRIND=1
> ...
> #==54610== Syscall param write(buf) points to uninitialised byte(s)
> #==54610==at 0x6F63317: write (write.c:26)
> #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x9049479: MPID_Send (in /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8FC9B2A: MPIC_Send (in /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in 
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE2A6F: PMPI_Bcast (in 
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> #==54610==by 0x4B39291: PetscOptionsInsert (options.c:672)
> #==54610==by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> #==54610==by 0x10A6BA: main (ex9.c:75)
> #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> #==54610==  in frame #3, created by MPIDI_CH3_EagerCo

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Patrick Sanan 
It's not the most satisfying solution but you can also pretty quickly
generate and use suppression files to at least de-clutter the output:
https://valgrind.org/docs/manual/manual-core.html#manual-core.suppress

Am Di., 2. Juni 2020 um 18:59 Uhr schrieb Satish Balay via petsc-dev <
petsc-dev@mcs.anl.gov>:

> MPICH need to be built with the option --enable-g=meminit for it to be
> valgrind clean.
>
> --download-mpich does this [among other things that are useful during
> software developement]. Pre-configured MPICH is not likely to do this.
>
> You can verify with: mpichversion
>
> You can prebuild MPICH using PETSc with:
>
> ./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS=
> CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=
>
> And make this your default pre-installed MPI. [by adding $HOME/soft/mpich
> to PATH]
>
> Satish
>
>
> On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:
>
> > Yes I am using the pre-loaded MPICH from the docker image. Further proof
> from configure
> >
> > #define PETSC_HAVE_MPICH_NUMVERSION 30302300
> > #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
> >
> > Best regards,
> >
> > Jacob Faibussowitsch
> > (Jacob Fai - booss - oh - vitch)
> > Cell: (312) 694-3391
> >
> > > On Jun 2, 2020, at 11:35 AM, Junchao Zhang 
> wrote:
> > >
> > > I guess Jacob already used MPICH, since
> MPIDI_CH3_EagerContigShortSend() is from MPICH.
> > >
> > > --Junchao Zhang
> > >
> > >
> > > On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev <
> petsc-dev@mcs.anl.gov > wrote:
> > > use --download-mpich for valgrind.
> > >
> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
> > >
> > > Satish
> > >
> > > On Tue, 2 Jun 2020, Karl Rupp wrote:
> > >
> > > > Hi Jacob,
> > > >
> > > > the recommendation in the past was to use MPICH as it is (was?)
> > > > valgrind-clean. Which MPI do you use? OpenMPI used to have these
> kinds of
> > > > issues. (My information might be outdated)
> > > >
> > > > Best regards,
> > > > Karli
> > > >
> > > > On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > > > > Hello All,
> > > > >
> > > > > TL;DR: valgrind always complains about "Syscall param write(buf)
> points to
> > > > > uninitialised byte(s)” for a LOT of MPI operations in petsc code,
> making
> > > > > debugging using valgrind fairly annoying since I have to sort
> through a ton
> > > > > of unrelated stuff. I have built valgrind from source, used apt
> install
> > > > > valgrind, apt install valgrind-mpi to no avail.
> > > > >
> > > > > I am using valgrind from docker. Dockerfile is attached below as
> well. I
> > > > > have been unsuccessfully trying to resolve these local valgrind
> errors, but
> > > > > I am running out of ideas. Googling the issue has also not
> provided entirely
> > > > > applicable solutions. Here is an example of the error:
> > > > >
> > > > > $ make -f gmakefile test VALGRIND=1
> > > > > ...
> > > > > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > > > > #==54610==at 0x6F63317: write (write.c:26)
> > > > > #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x9049479: MPID_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8FC9B2A: MPIC_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x8EE2A6F: PMPI_Bcast (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > > > > #==54610==by 0x4B39291: PetscOptionsInsert (options.c:672)
> > > > > #==54610==by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > > > > #==54610==by 0x10A6BA: main (ex9.c:75)
> > > > > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > > > > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend
> (???:)
> > > > > #==54610==  Uninitialised value was created by a stack allocation
> > > > > #==54610==at 0x903F200: MPIDI_CH3_EagerContigShortSend (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > >
> > > > > T

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Jacob Faibussowitsch 
> MPICH need to be built with the option --enable-g=meminit for it to be 
> valgrind clean.
I see. Two questions:

1. I am using Jeds docker image for MPICH (actually this is the main reason for 
using Jeds image, as configuring and building MPICH takes an absolute age on 
docker), will this re-build the MPICH already installed in the image or 
download and build an entirely new MPICH?

2. (More a question for Jed) If I am using Jeds docker image anyways and we 
have CI/CD builds also using his docker images (correct me if I am wrong here) 
and a valgrind build in stage 3 why not include those build arguments in the 
MPICH included in the images? I think the valgrind build for CI/CD actually 
downloads and builds MPICH through petsc configure, is this because of the 
errors I detailed below?

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391

> On Jun 2, 2020, at 11:59 AM, Satish Balay  wrote:
> 
> MPICH need to be built with the option --enable-g=meminit for it to be 
> valgrind clean.
> 
> --download-mpich does this [among other things that are useful during 
> software developement]. Pre-configured MPICH is not likely to do this.
> 
> You can verify with: mpichversion
> 
> You can prebuild MPICH using PETSc with:
> 
> ./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS= 
> CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=
> 
> And make this your default pre-installed MPI. [by adding $HOME/soft/mpich to 
> PATH]
> 
> Satish
> 
> 
> On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:
> 
>> Yes I am using the pre-loaded MPICH from the docker image. Further proof 
>> from configure
>> 
>> #define PETSC_HAVE_MPICH_NUMVERSION 30302300
>> #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
>> 
>> Best regards,
>> 
>> Jacob Faibussowitsch
>> (Jacob Fai - booss - oh - vitch)
>> Cell: (312) 694-3391
>> 
>>> On Jun 2, 2020, at 11:35 AM, Junchao Zhang  wrote:
>>> 
>>> I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() is 
>>> from MPICH. 
>>> 
>>> --Junchao Zhang
>>> 
>>> 
>>> On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev 
>>> mailto:petsc-dev@mcs.anl.gov> 
>>> >> wrote:
>>> use --download-mpich for valgrind.
>>> 
>>> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
>>> >>  >
>>> 
>>> Satish
>>> 
>>> On Tue, 2 Jun 2020, Karl Rupp wrote:
>>> 
 Hi Jacob,
 
 the recommendation in the past was to use MPICH as it is (was?)
 valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
 issues. (My information might be outdated)
 
 Best regards,
 Karli
 
 On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> Hello All,
> 
> TL;DR: valgrind always complains about "Syscall param write(buf) points to
> uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> debugging using valgrind fairly annoying since I have to sort through a 
> ton
> of unrelated stuff. I have built valgrind from source, used apt install
> valgrind, apt install valgrind-mpi to no avail.
> 
> I am using valgrind from docker. Dockerfile is attached below as well. I
> have been unsuccessfully trying to resolve these local valgrind errors, 
> but
> I am running out of ideas. Googling the issue has also not provided 
> entirely
> applicable solutions. Here is an example of the error:
> 
> $ make -f gmakefile test VALGRIND=1
> ...
> #==54610== Syscall param write(buf) points to uninitialised byte(s)
> #==54610==at 0x6F63317: write (write.c:26)
> #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x9049479: MPID_Send (in /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8FC9B2A: MPIC_Send (in /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in 
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> /usr/local/lib/libmpi.so.12.1.8)
> #==54610==by 0x8EE2A6F: PMPI_Bcast (in 
> /usr/local/lib/libmpi.so.12.1.

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Satish Balay via petsc-dev 
MPICH need to be built with the option --enable-g=meminit for it to be valgrind 
clean.

--download-mpich does this [among other things that are useful during software 
developement]. Pre-configured MPICH is not likely to do this.

You can verify with: mpichversion

You can prebuild MPICH using PETSc with:

./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS= 
CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=

And make this your default pre-installed MPI. [by adding $HOME/soft/mpich to 
PATH]

Satish


On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:

> Yes I am using the pre-loaded MPICH from the docker image. Further proof from 
> configure
> 
> #define PETSC_HAVE_MPICH_NUMVERSION 30302300
> #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
> 
> Best regards,
> 
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
> Cell: (312) 694-3391
> 
> > On Jun 2, 2020, at 11:35 AM, Junchao Zhang  wrote:
> > 
> > I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() is 
> > from MPICH. 
> > 
> > --Junchao Zhang
> > 
> > 
> > On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev 
> > mailto:petsc-dev@mcs.anl.gov>> wrote:
> > use --download-mpich for valgrind.
> > 
> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
> > 
> > 
> > Satish
> > 
> > On Tue, 2 Jun 2020, Karl Rupp wrote:
> > 
> > > Hi Jacob,
> > > 
> > > the recommendation in the past was to use MPICH as it is (was?)
> > > valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
> > > issues. (My information might be outdated)
> > > 
> > > Best regards,
> > > Karli
> > > 
> > > On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > > > Hello All,
> > > > 
> > > > TL;DR: valgrind always complains about "Syscall param write(buf) points 
> > > > to
> > > > uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> > > > debugging using valgrind fairly annoying since I have to sort through a 
> > > > ton
> > > > of unrelated stuff. I have built valgrind from source, used apt install
> > > > valgrind, apt install valgrind-mpi to no avail.
> > > > 
> > > > I am using valgrind from docker. Dockerfile is attached below as well. I
> > > > have been unsuccessfully trying to resolve these local valgrind errors, 
> > > > but
> > > > I am running out of ideas. Googling the issue has also not provided 
> > > > entirely
> > > > applicable solutions. Here is an example of the error:
> > > > 
> > > > $ make -f gmakefile test VALGRIND=1
> > > > ...
> > > > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > > > #==54610==at 0x6F63317: write (write.c:26)
> > > > #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x9049479: MPID_Send (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8FC9B2A: MPIC_Send (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x8EE2A6F: PMPI_Bcast (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > #==54610==by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > > > #==54610==by 0x4B39291: PetscOptionsInsert (options.c:672)
> > > > #==54610==by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > > > #==54610==by 0x10A6BA: main (ex9.c:75)
> > > > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > > > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend 
> > > > (???:)
> > > > #==54610==  Uninitialised value was created by a stack allocation
> > > > #==54610==at 0x903F200: MPIDI_CH3_EagerContigShortSend (in 
> > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > 
> > > > There are probably 20 such errors every single time, regardless of what 
> > > > code
> > > > is being run. I have tried using apt install valgrind, apt install
> > > > valgrind-mpi, and building valgrind from source:
> > > > 
> > > > # VALGRIND
> > > > WORKDIR /
> > > > RUN git clone git://sourceware.org/git/valgrind.git 
> > > > 
> > > > WORKDIR /valgrind
> > > > RUN git pull
> > > > RUN ./autogen.sh
> > > > RUN

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Jacob Faibussowitsch 
Yes I am using the pre-loaded MPICH from the docker image. Further proof from 
configure

#define PETSC_HAVE_MPICH_NUMVERSION 30302300
#define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391

> On Jun 2, 2020, at 11:35 AM, Junchao Zhang  wrote:
> 
> I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() is 
> from MPICH. 
> 
> --Junchao Zhang
> 
> 
> On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev 
> mailto:petsc-dev@mcs.anl.gov>> wrote:
> use --download-mpich for valgrind.
> 
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
> 
> 
> Satish
> 
> On Tue, 2 Jun 2020, Karl Rupp wrote:
> 
> > Hi Jacob,
> > 
> > the recommendation in the past was to use MPICH as it is (was?)
> > valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
> > issues. (My information might be outdated)
> > 
> > Best regards,
> > Karli
> > 
> > On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > > Hello All,
> > > 
> > > TL;DR: valgrind always complains about "Syscall param write(buf) points to
> > > uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> > > debugging using valgrind fairly annoying since I have to sort through a 
> > > ton
> > > of unrelated stuff. I have built valgrind from source, used apt install
> > > valgrind, apt install valgrind-mpi to no avail.
> > > 
> > > I am using valgrind from docker. Dockerfile is attached below as well. I
> > > have been unsuccessfully trying to resolve these local valgrind errors, 
> > > but
> > > I am running out of ideas. Googling the issue has also not provided 
> > > entirely
> > > applicable solutions. Here is an example of the error:
> > > 
> > > $ make -f gmakefile test VALGRIND=1
> > > ...
> > > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > > #==54610==at 0x6F63317: write (write.c:26)
> > > #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x9049479: MPID_Send (in /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8FC9B2A: MPIC_Send (in /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in 
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE2A6F: PMPI_Bcast (in 
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > > #==54610==by 0x4B39291: PetscOptionsInsert (options.c:672)
> > > #==54610==by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > > #==54610==by 0x10A6BA: main (ex9.c:75)
> > > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend (???:)
> > > #==54610==  Uninitialised value was created by a stack allocation
> > > #==54610==at 0x903F200: MPIDI_CH3_EagerContigShortSend (in 
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > 
> > > There are probably 20 such errors every single time, regardless of what 
> > > code
> > > is being run. I have tried using apt install valgrind, apt install
> > > valgrind-mpi, and building valgrind from source:
> > > 
> > > # VALGRIND
> > > WORKDIR /
> > > RUN git clone git://sourceware.org/git/valgrind.git 
> > > 
> > > WORKDIR /valgrind
> > > RUN git pull
> > > RUN ./autogen.sh
> > > RUN ./configure --with-mpicc=/usr/local/bin/mpicc
> > > RUN make -j 5
> > > RUN make install
> > > 
> > > None of the those approaches lead to these errors disappearing. Perhaps I 
> > > am
> > > missing some funky MPI args?
> > > 
> > > Best regards,
> > > 
> > > Jacob Faibussowitsch
> > > (Jacob Fai - booss - oh - vitch)
> > > Cell: (312) 694-3391
> > > 
> > > 
> > 
> >

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Junchao Zhang 
I guess Jacob already used MPICH, since MPIDI_CH3_EagerContigShortSend() is
from MPICH.

--Junchao Zhang


On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev <
petsc-dev@mcs.anl.gov> wrote:

> use --download-mpich for valgrind.
>
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> Satish
>
> On Tue, 2 Jun 2020, Karl Rupp wrote:
>
> > Hi Jacob,
> >
> > the recommendation in the past was to use MPICH as it is (was?)
> > valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
> > issues. (My information might be outdated)
> >
> > Best regards,
> > Karli
> >
> > On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > > Hello All,
> > >
> > > TL;DR: valgrind always complains about "Syscall param write(buf)
> points to
> > > uninitialised byte(s)” for a LOT of MPI operations in petsc code,
> making
> > > debugging using valgrind fairly annoying since I have to sort through
> a ton
> > > of unrelated stuff. I have built valgrind from source, used apt install
> > > valgrind, apt install valgrind-mpi to no avail.
> > >
> > > I am using valgrind from docker. Dockerfile is attached below as well.
> I
> > > have been unsuccessfully trying to resolve these local valgrind
> errors, but
> > > I am running out of ideas. Googling the issue has also not provided
> entirely
> > > applicable solutions. Here is an example of the error:
> > >
> > > $ make -f gmakefile test VALGRIND=1
> > > ...
> > > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > > #==54610==at 0x6F63317: write (write.c:26)
> > > #==54610==by 0x9056AC9: MPIDI_CH3I_Sock_write (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x9049479: MPID_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8FC9B2A: MPIC_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8F86F2E: MPIR_Bcast_intra_binomial (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE21F4: MPIR_Bcast_impl (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x8EE2A6F: PMPI_Bcast (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > #==54610==by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > > #==54610==by 0x4B39291: PetscOptionsInsert (options.c:672)
> > > #==54610==by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > > #==54610==by 0x10A6BA: main (ex9.c:75)
> > > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend
> (???:)
> > > #==54610==  Uninitialised value was created by a stack allocation
> > > #==54610==at 0x903F200: MPIDI_CH3_EagerContigShortSend (in
> > > /usr/local/lib/libmpi.so.12.1.8)
> > >
> > > There are probably 20 such errors every single time, regardless of
> what code
> > > is being run. I have tried using apt install valgrind, apt install
> > > valgrind-mpi, and building valgrind from source:
> > >
> > > # VALGRIND
> > > WORKDIR /
> > > RUN git clone git://sourceware.org/git/valgrind.git
> > > WORKDIR /valgrind
> > > RUN git pull
> > > RUN ./autogen.sh
> > > RUN ./configure --with-mpicc=/usr/local/bin/mpicc
> > > RUN make -j 5
> > > RUN make install
> > >
> > > None of the those approaches lead to these errors disappearing.
> Perhaps I am
> > > missing some funky MPI args?
> > >
> > > Best regards,
> > >
> > > Jacob Faibussowitsch
> > > (Jacob Fai - booss - oh - vitch)
> > > Cell: (312) 694-3391
> > >
> > >
> >
> >
>

Re: [petsc-dev] Valgrind MPI-Related Errors

2020-06-02 Thread Satish Balay via petsc-dev 
use --download-mpich for valgrind.

https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

Satish

On Tue, 2 Jun 2020, Karl Rupp wrote:

> Hi Jacob,
> 
> the recommendation in the past was to use MPICH as it is (was?)
> valgrind-clean. Which MPI do you use? OpenMPI used to have these kinds of
> issues. (My information might be outdated)
> 
> Best regards,
> Karli
> 
> On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > Hello All,
> > 
> > TL;DR: valgrind always complains about "Syscall param write(buf) points to
> > uninitialised byte(s)” for a LOT of MPI operations in petsc code, making
> > debugging using valgrind fairly annoying since I have to sort through a ton
> > of unrelated stuff. I have built valgrind from source, used apt install
> > valgrind, apt install valgrind-mpi to no avail.
> > 
> > I am using valgrind from docker. Dockerfile is attached below as well. I
> > have been unsuccessfully trying to resolve these local valgrind errors, but
> > I am running out of ideas. Googling the issue has also not provided entirely
> > applicable solutions. Here is an example of the error:
> > 
> > $ make -f gmakefile test VALGRIND=1
> > ...
> > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > #==54610==    at 0x6F63317: write (write.c:26)
> > #==54610==    by 0x9056AC9: MPIDI_CH3I_Sock_write (in 
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x9049479: MPID_Send (in /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8FC9B2A: MPIC_Send (in /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8F86F2E: MPIR_Bcast_intra_binomial (in 
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8EE21F4: MPIR_Bcast_impl (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8EE21F4: MPIR_Bcast_impl (in
> > /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x8EE2A6F: PMPI_Bcast (in /usr/local/lib/libmpi.so.12.1.8)
> > #==54610==    by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > #==54610==    by 0x4B39291: PetscOptionsInsert (options.c:672)
> > #==54610==    by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > #==54610==    by 0x10A6BA: main (ex9.c:75)
> > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend (???:)
> > #==54610==  Uninitialised value was created by a stack allocation
> > #==54610==    at 0x903F200: MPIDI_CH3_EagerContigShortSend (in 
> > /usr/local/lib/libmpi.so.12.1.8)
> > 
> > There are probably 20 such errors every single time, regardless of what code
> > is being run. I have tried using apt install valgrind, apt install
> > valgrind-mpi, and building valgrind from source:
> > 
> > # VALGRIND
> > WORKDIR /
> > RUN git clone git://sourceware.org/git/valgrind.git
> > WORKDIR /valgrind
> > RUN git pull
> > RUN ./autogen.sh
> > RUN ./configure --with-mpicc=/usr/local/bin/mpicc
> > RUN make -j 5
> > RUN make install
> > 
> > None of the those approaches lead to these errors disappearing. Perhaps I am
> > missing some funky MPI args?
> > 
> > Best regards,
> > 
> > Jacob Faibussowitsch
> > (Jacob Fai - booss - oh - vitch)
> > Cell: (312) 694-3391
> > 
> > 
> 
>