Problems to parallelization

[Eduardo López]

Hi everyone, 

I'm using NWChem (7.0.2) in my workstation (Centos 7) for some calculation of polarizability, when I run nwchem with the command nwchem input.nw >& output.out &, my calculation runs well and finishes without problems.

The problem is when I try with the command mpirun -np <#> $NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem input.nw >& output.out &, the process fails, this happens with all my inputs. 

With -np 1

MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

With -np 2

The process stop in the middle of the calculation.

With -np 3

argument  1 = nitrogeno.nw

With -np 4

NOTHING 

The way I compiled was the follow 

export NWCHEM_TOP=/home/nwchem/nwchem-7.0.2
export NWCHEM_TARGET=LINUX64
export USE_MPI=y
export USE_PYTHONCONFIG=y
export BLASOPT="-lopenblas -lpthread -lrt"
export LAPACK_LIB=$BLASOPT
export BLAS_SIZE=4
export PYTHONVERSION=3.6
export BLASOPT=-lopenblas  
export LAPACK_LIB=-lopenblas
export ARMCI_NETWORK=MPI-PR

make nwchem_config NWCHEM_MODULES="all python"

make

Thanks for your attention

Eduardo

[Edoardo Aprà]

You might want to skip the compilation step and use the precompiled binaries available through EPEL.

Installation instructions at

https://nwchemgit.github.io/Download.html#example-of-nwchem-rpm-installation-under-centos-7-x86_64

[Eduardo López]

Thanks I will try it 

[Shuqiang Niu]

Hi, Edo,

Could you give more details about using the precompiled binaries for installation?  I tried https://github.com/nwchemgit/nwchem/releases/tag/v7.0.2-release. It works great for Ubuntu 20.04 with an intel CPU. However, it doesn't work for Ubuntu 22.04 with AMD Ryzen CPU. 

Best

Shuqiang

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[Edoardo Aprà]

For ubuntu jammy, the following should work

sudo apt -y install python3-dev gfortran mpi-default-bin mpi-default-dev ssh

curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-data_7.2.0-1_all.ubuntu_jammy.deb

curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem_7.2.0-1_amd64.ubuntu_jammy.deb

sudo dpkg -i nwchem*7.2.0*jammy*.deb

Please let me know if it works on your Ryzen box.

To run, please use the following command (you might want to change the number of parallel process supplied with the -np argument)

mpirun.openmpi -np 2 nwchem

[Shuqiang Niu]

Hi, Edo,

Thanks for your suggestion. I tried the installation again with the new instruction. I got the message below.

john@john:~$ curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-data_7.2.0-1_all.ubuntu_jammy.deb

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100     9  100     9    0     0     52      0 --:--:-- --:--:-- --:--:--    52

john@john:~$ curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem_7.2.0-1_amd64.ubuntu_jammy.deb

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100     9  100     9    0     0     59      0 --:--:-- --:--:-- --:--:--    59

john@john:~$ sudo dpkg -i nwchem*7.2.0*jammy*.deb

dpkg-deb: error: 'nwchem_7.2.0-1_amd64.ubuntu_jammy.deb' is not a Debian format archive

dpkg: error processing archive nwchem_7.2.0-1_amd64.ubuntu_jammy.deb (--install):

 dpkg-deb --control subprocess returned error exit status 2

dpkg-deb: error: 'nwchem-data_7.2.0-1_all.ubuntu_jammy.deb' is not a Debian format archive

dpkg: error processing archive nwchem-data_7.2.0-1_all.ubuntu_jammy.deb (--install):

 dpkg-deb --control subprocess returned error exit status 2

Errors were encountered while processing:

 nwchem_7.2.0-1_amd64.ubuntu_jammy.deb

 nwchem-data_7.2.0-1_all.ubuntu_jammy.deb

Best

Shuqiang

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[Edoardo Aprà]

I  have uploaded a new version of the NWChem jammy packages.

Here are the updated instructions (available at https://github.com/nwchemgit/nwchem/releases, too)

sudo apt -y install  python3-dev gfortran  mpi-default-bin mpi-default-dev ssh

curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-data_7.2.0-2_all.ubuntu_jammy.deb
curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem_7.2.0-2_amd64.ubuntu_jammy.deb
sudo dpkg -i nwchem*7.2.0*jammy*.deb

[Edoardo Aprà]

Please remove the previously downloaded files (e.g. rm nwchem*jam*deb)

[Shuqiang Niu]

Hi, Edo,

I am wondering if the Openmpi 4.1.1 version supports this NWChem version. 

Thanks

Shuqiang

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[Edoardo Aprà]

I would recommend using OpenMPI 4.1.4 and later versions.

I have experience memory leaks with earlier versions of the OpenMPI 4.1.x series

[Shuqiang Niu]

I have to run some other software with Openmpi 4.1.1.

Shuqiang

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[Shuqiang Niu]

Hi, Edo,

I have reinstalled Ubuntu system followed by NWChem installation as instructed. The installation seems fine now. However, when I run NWChem, I got the message below:

john@John:~/test-nw$ mpirun.openmpi -np 2 nwchem h2o > h2o.out &

[1] 150438

john@John:~/test-nw$ [John:150438] *** Process received signal ***

[John:150438] Signal: Segmentation fault (11)

[John:150438] Signal code: Address not mapped (1)

[John:150438] Failing at address: (nil)

[John:150438] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fda7ec42520]

[John:150438] *** End of error message ***



[1]+  Segmentation fault      (core dumped) mpirun.openmpi -np 2 nwchem h2o > h2o.out

Shuqiang

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[Edoardo Aprà]

What is the output of the command

dpkg-query -l |egrep openmpi- | sort | cut -c 1-77

[Edoardo Aprà]

Could you post the h2o.nw file and the output of the command

free -m

[Edoardo Aprà]

Post the output of the command

which nwchem

[Shuqiang Niu]

john@John:~/test-nw$ which nwchem

/usr/bin/nwchem

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[Shuqiang Niu]

The input h2o is :

****************************************************************

start h2o

 title "Water in 6-31g basis set"



 geometry units au

   O      0.00000000    0.00000000    0.00000000

   H      0.00000000    1.43042809   -1.10715266

   H      0.00000000   -1.43042809   -1.10715266

 end

 basis

   H library 6-31g

   O library 6-31g

 end

 task scf optimize
****************************************************************

The output is empty.

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[Shuqiang Niu]

Hi, Edo,

You are right. After updating Openmpi to version 4.1.5, NWChem works.

Thanks.

Shuqiang

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[Shuqiang Niu]

Edo,

I tried to install nwchem again in ubuntu. After run: dpkg-query -l |egrep openmpi- | sort | cut -c 1-77

, I got

john@John:~/test-nw$ dpkg-query -l |egrep openmpi- | sort | cut -c 1-77

ii  libcaf-openmpi-3:amd64                     2.9.2-3                      

ii  libcoarrays-openmpi-dev:amd64              2.9.2-3                      

ii  libopenmpi-dev:amd64                       4.1.2-2ubuntu1                

ii  openmpi-bin                                4.1.2-2ubuntu1                

ii  openmpi-common                             4.1.2-2ubuntu1 

               
john@John:~/test-nw$ which nwchem

/usr/bin/nwchem

However, when I run the calculation, I got the problem again.

john@John:~/test-nw$ mpirun.openmpi -np 2 nwchem h2o > h2o.out &

[2] 2939

[1]   Segmentation fault      (core dumped) mpirun.openmpi -np 2 nwchem h2o > h2o.out

john@John:~/test-nw$ [John:02939] *** Process received signal ***

[John:02939] Signal: Segmentation fault (11)

[John:02939] Signal code: Address not mapped (1)

[John:02939] Failing at address: (nil)

[John:02939] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f847fc42520]

[John:02939] *** End of error message ***



[2]+  Segmentation fault      (core dumped) mpirun.openmpi -np 2 nwchem h2o > h2o.out

The output is empty.

Shuqiang

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[Shuqiang Niu]

Hi, Edo,

Never mind. There is a problem with installing Openmpi 4.1.5. I fixed the problem. NWChem works now.

Thanks.

Shuqiang