Molcas Forum

Raymond

Member

Registered: 2020-04-11

Posts: 2

Issue at Compiling OpenMolcas

Hi guys,

I'm trying to compile OpenMolcas on Linux Mint.
I have experienced few problems which I managed to somehow solve.
However, one final issue has got me stuck. I was hoping you guys can help me out.

I compiled OpenMolcas by making the build folder using the ccmake and the make install.
My first issue was that libga was not found by the ccmake. I fixed the problem by manually putting the path into the cmake list file (CMakeLists.txt).

  find_library (LIBGA ga libga.a libga.al
    PATHS ENV GAROOT GA_INCLUDE_PATH "/usr/bin/ga/lib"
    PATH_SUFFIXES lib
    NO_DEFAULT_PATH
  )

My second isssue was solved by manually adding -lpthread into the cmake list file.

  target_link_libraries (${prog}.exe ${MPI_C_LIBRARIES} -lpthread)

The third one arised when I tried to run molcas. Pymolcas could not be initiated outside the molcas source or the compiled directory.
I did set the MOLCAS environment to current path but still pymolcas refused to look up the path.

MOLCAS=/opt/molcas/

echo $MOLCAS

/opt/molcas/

I fixed the issue by adding the correct path to the pymolcas wrapper source file as the default value (molcas_wrapper.py).

    self.molcas = abspath(get_utf8('MOLCAS', default='/opt/molcas'))

running pymolcas at an arbitrary directory:

    MOLCAS has been found at /opt/molcas

this fixed the issue of running pymolcas outside the aforementioned directories.
However this problem seem to persist as running simple calculations crash by this error.

simple input "water.inp"

&GATEWAY
  coord=water.xyz
  basis=sto-3g
&SEWARD
&SCF

pymolcas water.inp -f

Traceback (most recent call last):
  File "/usr/local/sbin/pymolcas", line 595, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 134, in main
  File "/usr/lib/python3.6/os.py", line 669, in __getitem__
    raise KeyError(key) from None
KeyError: 'MOLCAS'

Please let me know if any of the solutions I found for my issues are causing this problem.
I suspect the path "MOLCAS" should somehow be defined but I can not figure out why it is not.

Thanks for your assistance

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: Issue at Compiling OpenMolcas

My first issue was that libga was not found by the ccmake.

It should be if you define the GAROOT variable within [c]cmake. If not, maybe the structure/version of your GA installation is different from what has been used so far.

My second isssue was solved by manually adding -lpthread into the cmake list file.

I think I usually see -lpthread added automatically by cmake. Maybe your compiler/environment is not well supported?

I did set the MOLCAS environment to current path but still pymolcas refused to look up the path.

You probably have to export the variable. Alternatively, create a directory called ".Molcas" (notice the dot and uppercase) in your home directory, and inside it a file called "molcas" with /opt/molcas as only content.

pymolcas water.inp -f

Traceback (most recent call last):
  File "/usr/local/sbin/pymolcas", line 595, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 134, in main
  File "/usr/lib/python3.6/os.py", line 669, in __getitem__
    raise KeyError(key) from None
KeyError: 'MOLCAS'

I don't see how this could result from an undefined MOLCAS. It looks like the whole os.environ is undefined?

Raymond

Member

Registered: 2020-04-11

Posts: 2

Re: Issue at Compiling OpenMolcas

It should be if you define the GAROOT variable within [c]cmake. If not, maybe the structure/version of your GA installation is different from what has been used so far.

I used the source code from the ga directly and compiled it.
If I remember correctly it compiles everything directly to "./bin/lib/"
I used PREFIX to install into "./bin/ga/" and set the path by ccmake.
However by some reason though the path is found the library is not found!
I think the "PATH_SUFFIXES lib" was being ignored.

I think I usually see -lpthread added automatically by cmake. Maybe your compiler/environment is not well supported?

I am not sure how could this happened?

-- C compiler: /usr/bin/cc
-- C compiler flags:  -std=gnu99 -O2
-- Fortran compiler: /usr/bin/f95
-- Fortran compiler flags:   -fno-aggressive-loop-optimizations -cpp -fdefault-integer-8 -O2

You probably have to export the variable. Alternatively, create a directory called ".Molcas" (notice the dot and uppercase) in your home directory, and inside it a file called "molcas" with /opt/molcas as only content.

Exporting the variable worked for me! Thanks for your input.

I don't see how this could result from an undefined MOLCAS. It looks like the whole os.environ is undefined?

This issue resolved itself after exporting the MOLCAS variable