Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

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Joaquin

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Nov 9, 2016, 1:58:32 PM11/9/16
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Deal all,

I hope someone help me. I want to run step-40, so I need trilinos and petsc. First, I'm trying to interface trilinos-12.6.2 with deal.II-8.4.1. My computer has a gnu 4.8.4 compiler. Everything is ok until the "make test". The five step failed.

Joaquin

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Nov 9, 2016, 2:04:57 PM11/9/16
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On Wednesday, November 9, 2016 at 2:58:32 PM UTC-4, Joaquin wrote:
Dear all,

I hope someone help me. I want to run step-40, so I need trilinos and petsc. First, I'm trying to interface trilinos-12.6.2 with deal.II-8.4.1. My computer has a gnu 4.8.4 compiler. Everything is ok until the "make test". The five step failed. I'm sending detailed.log and quicktests.log files.

 Thanks in advance.
Joaquín
detailed.log
quicktests.log

Timo Heister

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Nov 9, 2016, 2:06:36 PM11/9/16
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What errors are you seeing?
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Wolfgang Bangerth

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Nov 9, 2016, 2:51:54 PM11/9/16
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On 11/09/2016 12:04 PM, 'Joaquin' via deal.II User Group wrote:
>
> I hope someone help me. I want to run step-40, so I need trilinos
> and petsc. First, I'm trying to interface trilinos-12.6.2 with
> deal.II-8.4.1. My computer has a gnu 4.8.4 compiler. Everything is
> ok until the "make test". The five step failed. I'm sending
> detailed.log and quicktests.log files.
>
>
> Thanks in advance.

The error you show

/usr/bin/ld: warning: libmpi.so.1, needed by
/home/jomivalen/thesis/trilinos-12.6.2/lib/libmuelu-adapters.so, may
conflict with libmpi.so.12
../../lib/libdeal_II.g.so.8.4.1: undefined reference to
`Teuchos::details::safeCommFree(int*)'
../../lib/libdeal_II.g.so.8.4.1: undefined reference to
`Epetra_MpiComm::Epetra_MpiComm(int)'

suggests that you build Trilinos with a different MPI implementation
than you used for deal.II. This is not going to work.

Best
W>

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Joaquin M Valencia Bravo

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Nov 9, 2016, 4:46:40 PM11/9/16
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Thank you for your response:

Which version of trilinos may I use in my case?. I followed the instructions on page:

                                    https://www.dealii.org/8.4.1/external-libs/trilinos.html

although, it was for trilinos-12.0.1. Should I use the same version?. What suggestions could you give me?

Sincerely,
Joaquin





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Timo Heister

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Nov 9, 2016, 5:02:48 PM11/9/16
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12.4.x is probably tested the most, but 12.6.x should also work.

On Wed, Nov 9, 2016 at 4:46 PM, 'Joaquin M Valencia Bravo' via deal.II
User Group <dea...@googlegroups.com> wrote:
> Thank you for your response:
>
> Which version of trilinos may I use in my case?. I followed the instructions
> on page:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dealii.org_8.4.1_external-2Dlibs_trilinos.html&d=CwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=5kCI7s-1sdw2_x0AHqWqxtm7tXyDGPt9_hkjcPA0V5w&s=r3pGi_SAF_7iXX_JdSX3zI8VLMDkl9lVK8MxB0A96Dg&e=
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>>
>>
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>
>
>
>
> --
> Joaquin Valencia
> Graduate Student
>
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Wolfgang Bangerth

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Nov 9, 2016, 5:10:56 PM11/9/16
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On 11/09/2016 02:46 PM, 'Joaquin M Valencia Bravo' via deal.II User
Group wrote:
>
> Which version of trilinos may I use in my case?. I followed the
> instructions on page:
>
>
> https://www.dealii.org/8.4.1/external-libs/trilinos.html
>
> although, it was for trilinos-12.0.1. Should I use the same version?.
> What suggestions could you give me?

Joaquin,
you ask the wrong question. The issue is not whether you should use
Trilinos 12.0 or 12.4 or 12.6. The problem was that you compiled
Trilinos *with one version* of MPI, and deal.II *with another version*
of MPI. This is what you need to fix. You can continue the same version
of Trilinos, as long as you install it with the same MPI as you use for
deal.II.

Best
W.

Joaquin M Valencia Bravo

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Nov 9, 2016, 5:30:04 PM11/9/16
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I understand, but I don't know how to compile both of them with the same version. Could you please tell me the steps to do that?

Thanks for your time,
Joaquin

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Wolfgang Bangerth

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Nov 9, 2016, 5:31:24 PM11/9/16
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On 11/09/2016 03:30 PM, 'Joaquin M Valencia Bravo' via deal.II User
Group wrote:
>
> I understand, but I don't know how to compile both of them with the same
> version. Could you please tell me the steps to do that?

Well, how did you compile the two before? :-) Presumably you used some
way to tell Trilinos which MPI to use, and some way to tell deal.II
which MPI to use.

Joaquin M Valencia Bravo

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Nov 9, 2016, 5:44:30 PM11/9/16
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Apparently I used the same MPI by default for both of them.
In case of trilinos, I followed the next steps:
$   mkdir build
$   cd build
$   
cmake \
	-D Trilinos_ENABLE_Sacado=ON \
	-D Trilinos_ENABLE_MueLu:BOOL=ON \
	-D Trilinos_ENABLE_Stratimikos=ON \
	-D CMAKE_BUILD_TYPE=RELEASE \
	-D CMAKE_CXX_FLAGS="-g -O3" \
	-D CMAKE_C_FLAGS="-g -O3" \
	-D CMAKE_FORTRAN_FLAGS="-g -O5" \
	-D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
	-D CMAKE_VERBOSE_MAKEFILE=FALSE \
	-D Trilinos_VERBOSE_CONFIGURE=FALSE \
	-D TPL_ENABLE_MPI=ON \
	-D BUILD_SHARED_LIBS=ON \
	-D CMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \

In case of deal.II, I followed the next steps:
 $   mkdir build
 $   cd build
 $   cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II ../
 $   make -j8 install
 $   make test

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Wolfgang Bangerth

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Nov 9, 2016, 5:48:02 PM11/9/16
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On 11/09/2016 03:44 PM, 'Joaquin M Valencia Bravo' via deal.II User
Group wrote:
>
> cmake \
> -D Trilinos_ENABLE_Sacado=ON \
> -D Trilinos_ENABLE_MueLu:BOOL=ON \
> -D Trilinos_ENABLE_Stratimikos=ON \
> -D CMAKE_BUILD_TYPE=RELEASE \
> -D CMAKE_CXX_FLAGS="-g -O3" \
> -D CMAKE_C_FLAGS="-g -O3" \
> -D CMAKE_FORTRAN_FLAGS="-g -O5" \
> -D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
> -D CMAKE_VERBOSE_MAKEFILE=FALSE \
> -D Trilinos_VERBOSE_CONFIGURE=FALSE \
> -D TPL_ENABLE_MPI=ON \
> -D BUILD_SHARED_LIBS=ON \
> -D CMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \
>
>
> In case of deal.II, I followed the next steps:
> $ mkdir build
> $ cd build
> $ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II ../

Does this build deal.II with MPI? If you enter the last command, it will
provide you with a summary at the end that states whether MPI was used
or not.

Joaquin M Valencia Bravo

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Nov 9, 2016, 5:52:30 PM11/9/16
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Apparently I used the same MPI by default for both of them.

In case of trilinos, I followed the next steps:
$  mkdir build
$  cd build
$ 
        cmake \
	-DTrilinos_ENABLE_Sacado=ON \
	-DTrilinos_ENABLE_MueLu:BOOL=ON \
	-DTrilinos_ENABLE_Stratimikos=ON \
	-DCMAKE_BUILD_TYPE=RELEASE \
	-DCMAKE_CXX_FLAGS="-g -O3" \
	-DCMAKE_C_FLAGS="-g -O3" \
	-DCMAKE_FORTRAN_FLAGS="-g -O5" \
	-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
	-DCMAKE_VERBOSE_MAKEFILE=FALSE \
	-DTrilinos_VERBOSE_CONFIGURE=FALSE \
	-DTPL_ENABLE_MPI=ON \
	-DBUILD_SHARED_LIBS=ON \
	-DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \
$ make -j8 install

In case of dealii, I followed the next steps:

$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
        -DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \
        -DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../
$ make -j8 install
$ make test (failed)

Thank you for your patience,
Joaquin

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Joaquin M Valencia Bravo

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Nov 9, 2016, 5:55:23 PM11/9/16
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Apparently I used the MPI by default for both of them.

In case of trilinos, I followed the next steps:
$  mkdir build
$  cd build
$ 
        cmake \
	-DTrilinos_ENABLE_Sacado=ON \
	-DTrilinos_ENABLE_MueLu:BOOL=ON \
	-DTrilinos_ENABLE_Stratimikos=ON \
	-DCMAKE_BUILD_TYPE=RELEASE \
	-DCMAKE_CXX_FLAGS="-g -O3" \
	-DCMAKE_C_FLAGS="-g -O3" \
	-DCMAKE_FORTRAN_FLAGS="-g -O5" \
	-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
	-DCMAKE_VERBOSE_MAKEFILE=FALSE \
	-DTrilinos_VERBOSE_CONFIGURE=FALSE \
	-DTPL_ENABLE_MPI=ON \
	-DBUILD_SHARED_LIBS=ON \
	-DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \
$ make -j8 install

In case of dealii, I followed the next steps:

$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
        -DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \
        -DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../
$ make -j8 install
$ make test (failed)

Thank you for your patience,
Joaquin
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Wolfgang Bangerth

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Nov 9, 2016, 5:56:32 PM11/9/16
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On 11/09/2016 03:52 PM, 'Joaquin M Valencia Bravo' via deal.II User
That's interesting then. Can you try to do
ldd $HOME/share/trilinos/lib/libepetra.so.12.6.2
ldd /home/jomivalen/cfem/deal.II/lib/libdeal_II.g.so.8.4.1
and in both cases see which MPI libraries they link to? For example, for
me this yields the following:

rilinos-12.8.1/lib> ldd libepetra.so.12.8.1 | grep mpi
libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1
(0x00007f1107a5f000)
libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12
(0x00007f110780b000)
libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1
(0x00007f1107091000)
libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12
(0x00007f1106dad000)
libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12
(0x00007f1105d31000)
libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13
(0x00007f1105a8e000)
rilinos-12.8.1/lib> cd
f/bangerth> cd p/deal.II/1/build/lib/
build/lib> ldd libdeal_II.so.8.5.0-pre | grep mpi
libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1
(0x00007f7e22f28000)
libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12
(0x00007f7e22181000)
libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1
(0x00007f7e152ff000)
libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12
(0x00007f7e150ab000)
libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12
(0x00007f7e148cf000)
libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13
(0x00007f7e1462c000

So they are the same.

Joaquin M Valencia Bravo

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Nov 9, 2016, 7:35:24 PM11/9/16
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Sorry for the late answer. I had to re-install dealii + trilinos.

jomivalen@Nalia ~/cfem/trilinos/lib $ ldd libepetra.so.12.6.2 | grep mpi
    libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007fb4ac8f7000)
    libmpi.so.1 => /usr/lib/libmpi.so.1 (0x00007fb4ac576000)

jomivalen@Nalia ~/thesis/dealii-8.4.1/build/lib $ ldd libdeal_II.g.so.8.4.1 | grep mpi
    libmpicxx.so.12 => /home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00007f75b64c3000)
    libmpi.so.12 => /home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpi.so.12 (0x00007f75b3855000)
    libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007f75ae037000)
    libmpi.so.1 => /usr/lib/libmpi.so.1 (0x00007f75adcb5000)

What does these results mean?. What should i do?

Thanks,
Joaquin

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Jean-Paul Pelteret

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Nov 10, 2016, 8:54:55 AM11/10/16
to deal.II User Group
Dear Joaquin,

It been a while since I've compiled trilinos manually, but if nothings changed since version 11.4 then your should be able to specify which MPI trilinos should be compiled against using the following cmake parameters:

-D TPL_ENABLE_MPI:BOOL=ON \
-D MPI_BASE_DIR:PATH=$DIR_BASE/OpenMPI/build/ \
-D CMAKE_CXX_COMPILER:FILEPATH=mpicxx \
-D CMAKE_C_COMPILER:FILEPATH=mpicc \
-D CMAKE_Fortran_COMPILER:FILEPATH=mpif90 \
-D Trilinos_EXTRA_LINK_FLAGS:STRING="-lgfortran" \

Note that you should of course change their values as is appropriate for your setup. Presumably this means at the very least setting the MPI base directory to "/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/".

Regards,
Jean-Paul

Wolfgang Bangerth

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Nov 10, 2016, 11:06:53 AM11/10/16
to dea...@googlegroups.com
On 11/09/2016 05:35 PM, 'Joaquin M Valencia Bravo' via deal.II User
Group wrote:
>
> jomivalen@Nalia ~/cfem/trilinos/lib $ ldd libepetra.so.12.6.2 | grep mpi
> libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007fb4ac8f7000)
> libmpi.so.1 => /usr/lib/libmpi.so.1 (0x00007fb4ac576000)
>
> jomivalen@Nalia ~/thesis/dealii-8.4.1/build/lib $ ldd
> libdeal_II.g.so.8.4.1 | grep mpi
> libmpicxx.so.12 =>
> /home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpicxx.so.12
> (0x00007f75b64c3000)
> libmpi.so.12 =>
> /home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpi.so.12
> (0x00007f75b3855000)
> libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007f75ae037000)
> libmpi.so.1 => /usr/lib/libmpi.so.1 (0x00007f75adcb5000)
>
> What does these results mean?. What should i do?

Since the second of your questions was already answered, let me answer
the first one (what does it mean?).

You happen to have two different MPI installations on your system. One
is apparently the one provided by Intel as part of the Intel compilers
that you have installed on your system. The other one is just a regular
MPI implementation in the standard /usr/lib directories. Apparently,
when you built Trilinos, the Trilinos cmake configurationi scripts chose
to use the regular MPI implementation. But for some reason, when you
built deal.II, the deal.II cmake configuration scripts chose the Intel MPI.

I don't know why that happens. It is possible, for example, that your
$PATH includes both /usr/bin and
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/bin,
and that in one directory you have an executable mpic++ and in the other
mpicxx. Usually, they are interchangeable, and we just search for the
first one we find. I assume that Trilinos does the same. If they search
in a different order, then Trilinos finds one and deal.II finds the
other one. If that's the case, then it is probably a bad idea to have
both of these MPI implementations accessible by default.

It is also possible that you loaded one module when you built Trilinos,
but another when you built deal.II.

Joaquin M Valencia Bravo

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Nov 10, 2016, 6:12:35 PM11/10/16
to dea...@googlegroups.com
Thanks to all for your suggestions and explanations.

I already installed and configured dealii + trilinos and passed the 5 steps after doing make test. The way I did that is:

1. I delete the intel compiler directory.
2. I follow the same steps as I sent in my message above.

My question now is if it will be there any negative consequences after I removed the intel directory. Everytime I open the terminal appears the next message:

bash: /home/jomivalen/intel/compilers_and_libraries/linux/bin/compilervars.sh: No such file or directory

Now I'm going to configure and install petsc and p4est.

Best,
Joaquín


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Wolfgang Bangerth

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Nov 10, 2016, 6:28:15 PM11/10/16
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On 11/10/2016 04:12 PM, 'Joaquin M Valencia Bravo' via deal.II User
Group wrote:
>
> bash:
> /home/jomivalen/intel/compilers_and_libraries/linux/bin/compilervars.sh:
> No such file or directory

You reference this file in your ~/.bashrc script. Just remove the line
in that script that reference the 'compilervars.sh' file.

Denis Davydov

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Nov 17, 2016, 7:49:52 AM11/17/16
to deal.II User Group


On Wednesday, November 9, 2016 at 11:44:30 PM UTC+1, Joaquin wrote:
Apparently I used the same MPI by default for both of them.

Not necessarily. You need to check logs to see what is picked up by Trilinos and what is picked up by deal.II.
To make sure both use the same MPI you can do:

-DCMAKE_C_COMPILER=
-DCMAKE_CXX_COMPILER=
-DCMAKE_Fortran_COMPILER=

to point to MPI compiler wrappers in deal.II and set

-DMPI_BASE_DIR:PATH=
-DTPL_ENABLE_MPI:BOOL=ON

in Trilinos.

If you still have problems, another option is to use tools to build the stack of software, such as 
and

Regards,
Denis.

Yi-Chung Chen

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Nov 17, 2016, 4:58:11 PM11/17/16
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I have similar experience. I solved it is by installing a local MPICH or OPENMPI (you can only have one), then export it to PATH.

BR
YC Chen
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