Molcas Forum

sourav ghoshal

Member

Registered: 2017-09-21

Posts: 25

Need help for Openmolcas Installation

Can anyone guide me how to install OpenMolcas? I have tried several times by following the instruction given in https://gitlab.com/Molcas/OpenMolcas. But, every time, I failed in "pymolcas verify"-step. It shows command not found.

May be I have missed to install any other submodule or any essential library files. I have CENTOS 7 os.

It will be very much helpful for me, if anyone instruct me the process of openmolcas installation in a step-wise manner. Thanks in advance....

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Need help for Openmolcas Installation

Check the messages when you run cmake, maybe you are missing some python packages and pymolcas is not being built. In addition, check the output of make, it will tell you whether pymolcas is being installed or you have to copy it manually somewhere in your path.

sourav ghoshal

Member

Registered: 2017-09-21

Posts: 25

Re: Need help for Openmolcas Installation

Thanks a lot. I have build pymolcas.

I found pymolcas installed in home/sghoshal//Software/usr/bin/. I export the pymolcas path in .bashrc and alias as 'molcas'.

Now, I got the following error...

Traceback (most recent call last):
  File "/home/sghoshal//Software/usr/bin/pymolcas", line 225, in <module>
    from molcas_aux import which
ImportError: No module named molcas_aux

------------------------------------------------------------------------------------------------------------------------------------------------------------------------
During cmake ../OpenMolcas. I got following...

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

-- Found PythonInterp: /opt/rh/rh-python36/root/usr/bin/python3 (found suitable version "3.6.3", minimum required is "3.0") 
Configuring compilers:
-- The Fortran compiler identification is GNU
-- The C compiler identification is GNU 4.8.5
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
Detecting Molcas version info:
-- OPENMOLCAS_VERSION: v18.09-617-g5a96a25
Detecting system info:
-- OS: Linux-x86_64
-- ADDRMODE: 64
-- PLATFORM: LINUX64
Configuring HDF5 support:
-- Could NOT find HDF5 (missing:  HDF5_LIBRARIES HDF5_INCLUDE_DIRS) 
-- HDF5 not found, it will be deactivated
Configuring linear algebra libraries:
-- Using Molcas' LAPACK+BLAS libraries (SLOW!)
-- LINALG_LIBRARIES: lapack;blas
Gromacs interface DISABLED
BLOCK interface DISABLED
CHEMPS2 interface DISABLED
MSYM support DISABLED
DMRG support DISABLED
HDF5 QCMaquis interface DISABLED
NECI interface DISABLED
EFP interface DISABLED
GEN1INT support DISABLED
libwfa support DISABLED
NEVPT2 support DISABLED
External GRID_IT DISABLED
Configuring runtime environment settings:
-- DEFMOLCASMEM:  2048
-- DEFMOLCASDISK: 20000
-- RUNSCRIPT:    $program $input
-- RUNBINARY:    $program
-- RUNBINARYSER: $program
Build type: Release
-- C compiler: /usr/bin/cc
-- C compiler flags:  -std=gnu99 -O2
-- Fortran compiler: /usr/bin/f95
-- Fortran compiler flags:  -cpp -fno-aggressive-loop-optimizations -fdefault-integer-8 -O2
-- Definitions: _MOLCAS_;_I8_;_LINUX_
-- Debug definitions: 
CMake Warning at Tools/pymolcas/CMakeLists.txt:35 (message):
  Some python modules are not available: pyparsing six

  pymolcas will be disabled


-- pymolcas: added to targets
Copying hook "/home/sghoshal/Software/openmolcas/OpenMolcas/sbin/pre-commit" into "/home/sghoshal/Software/openmolcas/OpenMolcas/.git/hooks/pre-commit"
Definitions: -D_MOLCAS_;-D_I8_;-D_LINUX_
Configuring documentation
-- Sphinx compiler: no sphinx-build available, documentation disabled
Install directory: /opt/molcas
-- Configuring done
-- Generating done
-- Build files have been written to: /home/sghoshal/Software/openmolcas/build

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

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Need help for Openmolcas Installation

Traceback (most recent call last):
  File "/home/sghoshal//Software/usr/bin/pymolcas", line 225, in <module>
    from molcas_aux import which
ImportError: No module named molcas_aux

That probably means it is the "source" file (just what you find in Tools/pymolcas), not the built stand-alone script.

CMake Warning at Tools/pymolcas/CMakeLists.txt:35 (message):
  Some python modules are not available: pyparsing six

  pymolcas will be disabled

That is the problem, you have to install those python packages.

sourav ghoshal

Member

Registered: 2017-09-21

Posts: 25

Re: Need help for Openmolcas Installation

Thanks a lot...

Yes... I have installed pyparsing and six modules of PYTHON.

I found following information after "make" in /build folder.
********************************************************************

pymolcas will be installed in /home/sghoshal/.openmpi/bin
Is this OK? [Y/n] (will assume "Yes" in 25 seconds)
yes^?^?^?^?
The installation of pymolcas was successful
[100%] Built target pymolcas

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

I found pymolcas in "/home/sghoshal/.openmpi/bin" directory.

What is the next step? How I will run my input file? How to submit job in multiple processors?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Need help for Openmolcas Installation

What is the next step? How I will run my input file? How to submit job in multiple processors?

Check the last sections in https://gitlab.com/Molcas/OpenMolcas/wi … ck%20start

For parallel calculations you can either define MOLCAS_NPROCS or use "pymolcas -np X".

sourav ghoshal

Member

Registered: 2017-09-21

Posts: 25

Re: Need help for Openmolcas Installation

Now, it showing "/home/sghoshal" is not a valid MOLCAS installation.... After typing pymolcas in terminal...

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Need help for Openmolcas Installation

You have to define the MOLCAS environment variable, or run pymolcas from the build directory.

sourav ghoshal

Member

Registered: 2017-09-21

Posts: 25

Re: Need help for Openmolcas Installation

Dear Ignacio,

I have successfully run pymolcas by specifying following in my bashrc...

export MOLCAS=/home/sghoshal/Software/molcas/build
export PATH=/home/sghoshal/.openmpi/bin:$PATH
alias molcas='/home/sghoshal/.openmpi/bin/pymolcas'

***********************************************************************************
Now, I have some few more quarries...

How to use multiple processor and increase RAM size for my calculation? How to change scratch directory from /tmp (default) to any specified directory (say my job submitting directory)?

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

I have gone through the pymolcas --setup command, which will create molcasrc file in .Molcas/ directory.

But, I could not understand that process clearly. It will be my pleasure, if you please guide me in that portion.

With Regards
Sourav

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Need help for Openmolcas Installation

Maybe you should read http://molcas.gitlab.io/OpenMolcas/sphi … nment.html

Note that some of the commands are specific to the "molcas" script, instead of "pymolcas", but most of it should work just the same.

Processors: "pymolcas -n" or MOLCAS_NPROCS
Memory: MOLCAS_MEM
Scratch: MOLCAS_WORKDIR