Molcas Forum

chucksty

Member

From: Cambridge, UK

Registered: 2019-07-13

Posts: 26

Website

OpenMolcas installed without installing pymolcas

Dear Molcas Team,
I had installed OpenMolcas be the default way of just running cmake without turning on other options like grid_it nevpt2 etc.
In an attempt to reinstall it, I sort of broke the code and messed up my exiting installation after running cmake with some other options turned on.

I decided to remove every single OpenMolcas folder including the original pymolcas. Below is the script I have used which might be useful for the community as well;

SCRIPT BEGINS HERE

#!/bin/bash

module purge
module load mkl/64/2019
module load ifort
module load anaconda/python2/5.3.0
module load cmake/3.16.3
module load armadillo/9.800.4

rm CMake* git*

export FC=ifort
export CC=icc
export CXX=icpc
export MKLROOT=/usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl

DIRNAME="$(dirname $(pwd))/OpenMolcas"
echo $DIRNAME
cmake -D CMAKE_INSTALL_PREFIX=/home/dci24/code/OpenPymolcas\
      -D MKLROOT=/usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl \
      -D LINALG=MKL \
      -D OPENMP=ON \
      -D GRID_IT=ON \
      -D NEVPT2=ON \
      -D WFA=ON\
      -D EFPLIB=ON\
      -D HDF5=ON \
      -D DMRG=ON \
      -D QCMaquis_NAME="chucksty" \
      -D QCMaquis_EMAIL="myemailaddresshere" \
      $DIRNAME

SCRIPT ENDS HERE

After some compatibility errors were sorted the programme seemed to have installed but surprisingly it didn't end with the part where it tells me where it wants to install pymolcas by asking if I want it there. Rather, see below as what I have.

-- Installing: /sharedscratch/dci24/code/molcas/build/qcmaquis/bin/mps_transform
-- Set runtime path of "/sharedscratch/dci24/code/molcas/build/qcmaquis/bin/mps_transform" to ""
-- Installing: /sharedscratch/dci24/code/molcas/build/qcmaquis/bin/mps_transform_pg
-- Set runtime path of "/sharedscratch/dci24/code/molcas/build/qcmaquis/bin/mps_transform_pg" to ""
[100%]  Creating a sourceable configuration file for QCMaquis/Boost/ALPS runtime environment settings that can be used with
 source /sharedscratch/dci24/code/molcas/build/qcmaquis/bin/qcmaquis.sh
 For further information on runtime environment settings please read the documentation carefully.
[100%]  Installation of QCMaquis, ALPS and Boost was successful!
 To run QCMaquis calculations (through Molcas) you have to adjust your paths as follows:
 export PATH=/sharedscratch/dci24/code/molcas/build/alps/bin:/sharedscratch/dci24/code/molcas/build/qcmaquis/bin:$PATH
 export PYTHONPATH=/sharedscratch/dci24/code/molcas/build/alps/lib:/sharedscratch/dci24/code/molcas/build/qcmaquis/lib/python/pyeval:/sharedscratch/dci24/code/molcas/build/qcmaquis/lib/python:$PYTHONPATH
 export LD_LIBRARY_PATH=/sharedscratch/dci24/code/molcas/build/alps/lib:$LD_LIBRARY_PATH
 For further information on please read the documentation carefully.
[100%] Completed 'qcmaquis'
[100%] Built target qcmaquis
[dc@cerebro build]$

What might have happened here? I can't seem to find pymolcas anywhere, make pymolcas doesn't work. It gives out a message saying "make: *** No rule to make target `pymolcas'.  Stop.". I also saw something like "$cp Tools/pymolcas/pymolcas_  /home/dci24/code/OpenPymolcas/bin/pymolcas" but that doesn't work because pymolcas_ doesn't exist at cp Tools/pymolcas/pymolcas_

Please, any idea what might have gone wrong?

Thanks

Chucksty

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: OpenMolcas installed without installing pymolcas

What does it tell you when you run cmake? If it doesn't find an appropriate python version or some package is missing, pymolcas will be disabled.

chucksty

Member

From: Cambridge, UK

Registered: 2019-07-13

Posts: 26

Website

Re: OpenMolcas installed without installing pymolcas

The problem is that DMRG requires python2 to compile, which why I am using python2. When I run cmake I get the following few lines.

-- Could NOT find PythonInterp: Found unsuitable version "2.7.15", but required is at least "3.0" (found /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/python)
-- Found PythonInterp: /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/python (found suitable version "2.7.15", minimum required is "2.7")
Configuring compilers:
-- The Fortran compiler identification is Intel 19.0.5.20190815
-- The C compiler identification is Intel 19.0.5.20190815
-- The CXX compiler identification is Intel 19.0.5.20190815
-- Check for working Fortran compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort
-- Check for working Fortran compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort supports Fortran 90
-- Checking whether /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort supports Fortran 90 -- yes
-- Check for working C compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icc
-- Check for working C compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icc -- works

Does it mean that pymolcas was disabled before the second line or the 2nd line is not related to correcting the first line?

What does it tell you when you run cmake? If it doesn't find an appropriate python version or some package is missing, pymolcas will be disabled.

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: OpenMolcas installed without installing pymolcas

This indicates python3 is searched first and not found, then python2 is searched and found. pymolcas should support python2, so that's fine. Look further down, it probably says "-- pymolcas: disabled" with some error above.

chucksty

Member

From: Cambridge, UK

Registered: 2019-07-13

Posts: 26

Website

Re: OpenMolcas installed without installing pymolcas

I can't seem to find anywhere it says pymolcas disabled when i run cmake. The only thing I have seen relating to pymolcas when cmake is run is as below.

CMake Warning at Tools/pymolcas/CMakeLists.txt:38 (message):
  Some python modules are not available: builtins|future.builtins

-- pymolcas: added to targets
Definitions: -D_MOLCAS_;-D_I8_;-D_LINUX_;-D_MKL_;-D_DMRG_;-D_EFP_
Configuring documentation
-- Sphinx compiler: /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/sphinx-build
-- LaTeX compiler: no latexmk available, pdf documentation disabled
Install directory: /home/dci24/code/OpenPymolcas
-- Configuring done
CMake Warning at CMakeLists.txt:2791 (add_executable):
  Cannot generate a safe runtime search path for target wfa.exe because files
  in some directories may conflict with libraries in implicit directories:

Also, there are other couple of warnings for all .exe files, some of which are below;

CMake Warning at CMakeLists.txt:2791 (add_executable):
  Cannot generate a safe runtime search path for target single_aniso.exe
  because files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libmkl_intel_ilp64.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_core.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_intel_thread.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib

  Some of these libraries may not be found correctly.


CMake Warning at CMakeLists.txt:2791 (add_executable):
  Cannot generate a safe runtime search path for target seward.exe because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libmkl_intel_ilp64.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_core.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_intel_thread.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib

  Some of these libraries may not be found correctly.

Does any of this mean any harm because the whole thing still manage through?
The cmake still finishes with the following last output that shows everything seems to have completed as one would expect.

CMake Warning at CMakeLists.txt:2791 (add_executable):
  Cannot generate a safe runtime search path for target slapaf.exe because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libmkl_intel_ilp64.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_core.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib
    runtime library [libmkl_intel_thread.so] in /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 may be hidden by files in:
      /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib

  Some of these libraries may not be found correctly.


-- Generating done
-- Build files have been written to: /home/dci24/software/molcas/build
[dci24@cerebro build]$ 

Regards
Chucksty

This indicates python3 is searched first and not found, then python2 is searched and found. pymolcas should support python2, so that's fine. Look further down, it probably says "-- pymolcas: disabled" with some error above.

Last edited by chucksty (2020-02-17 14:37:40)

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: OpenMolcas installed without installing pymolcas

OK, somehow it says it's added to targets, but it still shows there is some error:

CMake Warning at Tools/pymolcas/CMakeLists.txt:38 (message):
  Some python modules are not available: builtins|future.builtins

-- pymolcas: added to targets

You probably need to update the "future" python module

chucksty

Member

From: Cambridge, UK

Registered: 2019-07-13

Posts: 26

Website

Re: OpenMolcas installed without installing pymolcas

I have succeeded in runinning the cmake without any of those previous errors. See bellow for a complete terminal output.

rm: cannot remove `CMake*': No such file or directory
rm: cannot remove `git*': No such file or directory
/home/dci24/software/molcas/OpenMolcas
-- Could NOT find PythonInterp: Found unsuitable version "2.7.15", but required is at least "3.0" (found /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/python)
-- Found PythonInterp: /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/python (found suitable version "2.7.15", minimum required is "2.7")
Configuring compilers:
-- The Fortran compiler identification is Intel 19.0.5.20190815
-- The C compiler identification is Intel 19.0.5.20190815
-- The CXX compiler identification is Intel 19.0.5.20190815
-- Check for working Fortran compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort
-- Check for working Fortran compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort supports Fortran 90
-- Checking whether /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort supports Fortran 90 -- yes
-- Check for working C compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icc
-- Check for working C compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icpc
-- Check for working CXX compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icpc -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Detecting Molcas version info:
-- OPENMOLCAS_VERSION: v19.11-195-g854927e
Detecting system info:
-- OS: Linux-x86_64
-- ADDRMODE: 64
-- PLATFORM: LINUX64
Configuring HDF5 support:
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- Found HDF5: /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libhdf5_cpp.so;/usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.2") found components: C CXX
-- HDF5_INCLUDE_DIRS: /usr/local/shared/anylinux/anaconda/python2/5.3.0/include
-- HDF5_C_LIBRARIES: /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
-- HDF5_CXX_LIBRARIES: /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libhdf5_cpp.so;/usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
Configuring linear algebra libraries:
-- Using Intel Math Kernel Library (MKL)
-- MKLROOT = /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl
-- MKL_INCLUDE_PATH = /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/include
-- MKL_LIBRARY_PATH = /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64
-- LINALG_LIBRARIES: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_ilp64.so;/usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.so;/usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.so
Gromacs interface DISABLED
BLOCK interface DISABLED
CHEMPS2 interface DISABLED
MSYM support DISABLED
Configuring QCMaquis DMRG support:
-- Your name (used to download QCMaquis): David Chucksty
-- Your email (used to download QCMaquis): dci24@cam.ac.uk
-- QCMaquis DMRG not found. A pre-packaged version will be built.
--  Python 2: (for QCMaquis DMRG interface):
--   path   : /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/python2
--   version: 2.7
--  Python 2 libraries:
--   path    : /usr/local/shared/anylinux/anaconda/python2/5.3.0/lib/libpython2.7.so
--   Python.h: /usr/local/shared/anylinux/anaconda/python2/5.3.0/include/python2.7
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- Found GSL: /usr/include (found version "1.13")
-- Found OpenMP_C: -qopenmp (found version "5.0")
-- Found OpenMP_CXX: -qopenmp (found version "5.0")
-- Found OpenMP_Fortran: -qopenmp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0")
-- ALPS_ROOT and BOOST_ROOT: /home/dci24/software/molcas/build/alps
-- DMRG_INCLUDE_PATH: /home/dci24/software/molcas/build/mod
-- DMRG_LIBRARIES: /home/dci24/software/molcas/build/lib/libqcmaquis-driver-utils.a
Configuring HDF5 QCMaquis support:
-- HDF5_QCM_INCLUDE_PATH: /home/dci24/software/molcas/build/mod
-- HDF5_QCM_LIBRARIES: /home/dci24/software/molcas/build/lib/libHDF5interface.a
NECI interface DISABLED
Configuring EFP support:
-- EFP_LIBRARIES: efp
GEN1INT support DISABLED
Configuring libwfa support:
Configuring libwfa with Molcas objects included ...
-- wfa_libs: wfa_molcas
-- ARMADILLO_INC:
-- NEVPT2_LIBRARIES: /home/dci24/software/molcas/build/External/nevpt2_ext/src/nevpt2_ext-build/libqdnevpt2.a;/home/dci24/software/molcas/build/External/nevpt2_ext/src/nevpt2_ext-build/libAUXLIB_F.a
Configuring external GRID_IT:
-- Source found, external GRID_IT enabled
Configuring runtime environment settings:
-- DEFMOLCASMEM:  2048
-- DEFMOLCASDISK: 20000
-- RUNSCRIPT:    $program $input
-- RUNBINARY:    $program
-- RUNBINARYSER: $program
Build type: Release
-- C compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icc
-- C compiler flags:  -std=gnu99 -qopenmp -O2
-- Fortran compiler: /usr/local/shared/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/ifort
-- Fortran compiler flags:   -fpp -i8 -r8 -heap-arrays -qopenmp -O2 -traceback
-- Definitions: _MOLCAS_;_I8_;_LINUX_;_MKL_;_DMRG_;_EFP_
-- Debug definitions:
CMake Warning at Tools/pymolcas/CMakeLists.txt:38 (message):
  Some python modules are not available: builtins|future.builtins


-- pymolcas: added to targets
Definitions: -D_MOLCAS_;-D_I8_;-D_LINUX_;-D_MKL_;-D_DMRG_;-D_EFP_
Configuring documentation
-- Sphinx compiler: /usr/local/shared/anylinux/anaconda/python2/5.3.0/bin/sphinx-build
-- LaTeX compiler: no latexmk available, pdf documentation disabled
Install directory: /home/dci24/code/OpenPymolcas_2#
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dci24/software/molcas/build
[dci24@cerebro build]$

However, make doesn't seem to install pymolcas. Is there a way to install pymolcas after build?

Chucksty

OK, somehow it says it's added to targets, but it still shows there is some error:

CMake Warning at Tools/pymolcas/CMakeLists.txt:38 (message):
  Some python modules are not available: builtins|future.builtins

-- pymolcas: added to targets

You probably need to update the "future" python module

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: OpenMolcas installed without installing pymolcas

You still have the problem with missing builtins or future.builtins module.

chucksty

Member

From: Cambridge, UK

Registered: 2019-07-13

Posts: 26

Website

Re: OpenMolcas installed without installing pymolcas

No, I don't. For some reason, I installed pymolcas in a different workstation and scp to the cluster. However, on running the pymolcas verify I got many failed test but with the grayzone option and at the end, it says 1 critical failure. I am most concerned with the "3: Other test that may fail, but should be fixed" as listed below;

group grayzone from: /sharedscratch/dci24/code/molcas/OpenMolcas/test/grayzone
3:grayzone:067 Failed! (seward)
3:grayzone:068 Failed! (seward)
3:grayzone:116 OK
3:grayzone:139 Failed! (cpf)
3:grayzone:251 Failed! (rasscf)
3:grayzone:395 Failed! (rasscf)
3:grayzone:405 Failed! (seward)
3:grayzone:803 OK
3:grayzone:804 Failed! (scf)
3:grayzone:819 Failed! (seward)
3:grayzone:820 Failed! (scf)
3:grayzone:834 Skipped!
3:grayzone:850 Skipped!
3:grayzone:851 Skipped!
3:grayzone:860 OK
3:grayzone:861 Skipped!
----------

*Failed critical tests* 1

I also have  failed test for the "2: Additional tests that must pass" as below;

2:additional:835 Failed! (wfa)

Would any of these affect my calculation really?
Chucksty

You still have the problem with missing builtins or future.builtins module.

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: OpenMolcas installed without installing pymolcas

No, I don't.

According to the output you pasted, you do (for the python version that cmake was identifying).

However, on running the pymolcas verify I got many failed test but with the grayzone option and at the end, it says 1 critical failure. I am most concerned with the "3: Other test that may fail, but should be fixed"

You shouldn't be concerned. Grayzone tests are expected to fail (in some or all configurations). The "should be fixed" part is for developers.

I also have  failed test for the "2: Additional tests that must pass"

This is what you could be concerned about. This is the "failed critical test". Since it fails in WFA, it might be a bug in WFA, a instability in the test, or a problem with your installation. If you don't use WFA, you need not care, if you do, it depends on what is the kind of failure and why it's happening.