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#1 2018-07-16 16:59:11

hrgrimsl
Member
Registered: 2018-07-16
Posts: 8

pymolcas verify problems

I've followed the directions here:

https://gitlab.com/Molcas/OpenMolcas/bl … /README.md

but when I get to the "pymolcas verify" step, every test fails.  This occurs whether I run the test from the build directory or the cloned source directory.  Do I need to change my path or something to get this to work?

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#2 2018-07-16 17:07:52

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 558

Re: pymolcas verify problems

How does it fail? In the test/failed directory you should find *.out and *.err files, what do they say?

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#3 2018-07-16 17:12:33

hrgrimsl
Member
Registered: 2018-07-16
Posts: 8

Re: pymolcas verify problems

The error files give:

/home/harper/build/bin/gateway.exe: error while loading shared libraries: libhdf5.so.10: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/harper/psi4conda/bin/pymolcas", line 449, in <module>
    sys.exit(main(os.path.realpath(f)))
  File "<string>", line 206, in main
  File "<string>", line 686, in auto
  File "<string>", line 190, in run
  File "<string>", line 342, in run
  File "<string>", line 745, in run_module
  File "<string>", line 1203, in run
  File "<string>", line 1077, in _read_rc
  File "<string>", line 72, in utf8_open
FileNotFoundError: [Errno 2] No such file or directory: '/home/harper/build/test/tmp/standard__000/rc.global'

The output files give:

   This run of MOLCAS is using the pymolcas driver

                             OPE
                             OPE          NMOL  CASOP  ENMOLC A   SO
                 OPE        NMOLC        AS  OP EN  MO LC     AS  OP
                OPENM       OL CA        SO  PE NM  OL CA     SOP EN
                OP EN      MO   LC       AS  OP ENMOL  CASO   PENMOL
                OP  EN     MO   LC       AS  OP EN     MO     LC ASO
               OP   E  NMOL  C  AS       OP  EN MO     LC     AS  OP
               OP  E   NMO   LC AS        OPEN  MO     LCASOP EN   M
               O  PEN   MO  LCA  SO
            OPE   NMO   L   CAS    OP
        OPENMOL  CASOP     ENMOL   CASOPE
     OPENMOLCA   SOPENMOLCASOPEN   MOLCASOPE
    OPENMOLCAS   OP           EN   MOL    CAS
    OPENMOLCAS       OP  ENM        O     LCA
    OPENMOLCAS    OPEN  MOLCASO     P  E  NMO
    OPENMOLCAS     OP               E  N  MOL
    OPENMOLCA   SO           PENM   O  L  CAS    OPEN    MO    LCAS
    OPENMOLCA   SOP           ENM   O  L  CAS   OP  EN  MOLC  AS   O
    OPENMOLCA   SOPE           NM      O  LCA   S      OP  EN MO
    OPENMOLC                AS         O  PEN   M      OL  CA  SOPE
    OPENMO        LCASOPE  NMOL        C  ASO   P      ENMOLC     AS
    OPE     NMO      LCA  SO     P     E   NM   OL  CA SO  PE N   MO
          OPENMOLCA            SOPE   NMO        LCAS  O    P  ENMO
     OPENMOLCASOPENMOLCASOPENMOLCASOPENMOLCA
        OPENMOLCASOPENMOLCASOPENMOLCASOPE
            OPENMOLCASOPENMOLCASOPENM
               OPENMOLCASOPENMOLCA        version 18.0
                   OPENMOLCASO
                       OPE                tag o180711-1800

 OpenMolcas is free software; you can redistribute it and/or modify it
 under the terms of the GNU Lesser General Public License version 2.1.
 OpenMolcas is distributed in the hope that it will be useful, but it
 is provided "as is" and without any express or implied warranties.
 For more details see the full text of the license in the file
 LICENSE or in <[url]http://www.gnu.org/licenses/[/url]>.

                 Copyright (C) The OpenMolcas Authors
           For the author list and the recommended citation,
                   consult the file CONTRIBUTORS.md

           *************************************************
           * pymolcas version py2.03                       *
           *   build d8eddaaba1469419bf39e883732b37e3      *
           *   (after the EMIL interpreter by V. Veryazov) *
           *************************************************

configuration info
------------------
C Compiler ID: GNU
C flags: -std=gnu99
Fortran Compiler ID: GNU
Fortran flags: -cpp -fno-aggressive-loop-optimizations -fdefault-integer-8
Definitions: _MOLCAS_;_I8_;_LINUX_
Parallel: OFF (GA=OFF)


   -------------------------------------------------------------
  |
  |           Project: standard__000
  |    Submitted from: /home/harper/build/test/tmp
  |      Scratch area: /home/harper/build/test/tmp/standard__000
  |   Save outputs to: WORKDIR
  |            Molcas: /home/harper/build
  |
  | Scratch area is empty
  |
  |    MOLCAS_DRIVER = /home/harper/psi4conda/bin/pymolcas
  |      MOLCAS_GRID = NO
  |    MOLCAS_NPROCS = 1
  |    MOLCAS_SOURCE = /home/harper/OpenMolcas
  | MOLCAS_STRUCTURE = 0
  |   MOLCAS_TIMELIM = 600
  |
   -------------------------------------------------------------

++ ---------   Input file   ---------

>>> EXPORT MOLCAS_PRINT = VERBOSE

&GATEWAY
coord
2
angstrom
H  0.350000000  0.000000000  0.000000000
H -0.350000000  0.000000000  0.000000000
basis
h.DZ....
NoCD

&SEWARD

&SCF
Title
 H2, DZ Basis set

&RASSCF
Title
 H2, DZ Basis set
nActEl
 2  0 0
Ras2
 1 1 0 0 0 0 0 0

&ALASKA

&SLAPAF

&CASPT2
PROPerties

-- ----------------------------------

>>> EXPORT MOLCAS_PRINT = VERBOSE

--- Start Module: gateway at Mon Jul 16 11:52:07 2018 ---


Aborting...

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#4 2018-07-16 18:06:56

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 558

Re: pymolcas verify problems

You could have stopped with the first line:

/home/harper/build/bin/gateway.exe: error while loading shared libraries: libhdf5.so.10: cannot open shared object file: No such file or directory

Are you running in the same system and with the same environment where you compiled it?

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#5 2018-07-16 18:12:38

hrgrimsl
Member
Registered: 2018-07-16
Posts: 8

Re: pymolcas verify problems

I believe so.

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#6 2018-07-30 14:44:39

hrgrimsl
Member
Registered: 2018-07-16
Posts: 8

Re: pymolcas verify problems

I removed everything and tried reinstalling, but had an error with configuring via cmake.  Does anyone know how to deal with the following?

Configuring compilers:
Detecting Molcas version info:
-- OPENMOLCAS_VERSION: v17.0.o171117-1800-1-g8cc88dc
Detecting system info:
-- OS: Linux-x86_64
-- ADDRMODE: 64
-- PLATFORM: LINUX64
Configuring HDF5 support:
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
CMake Error at /usr/share/cmake-3.10/Modules/FindHDF5.cmake:252 (try_compile):
  Unknown extension ".cxx" for file

    /home/harper/build/CMakeFiles/hdf5/cmake_hdf5_test.cxx

  try_compile() works only for enabled languages.  Currently these are:

    C Fortran

  See project() command to enable other languages.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindHDF5.cmake:543 (_HDF5_test_regular_compiler_CXX)
  CMakeLists.txt:1075 (find_package)


-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- HDF5_INCLUDE_PATH: /home/harper/psi4conda/include
-- HDF5_LIBRARIES: /home/harper/psi4conda/lib/libhdf5_cpp.so;/home/harper/psi4conda/lib/libhdf5.so;rt;pthread;/home/harper/psi4conda/lib/libz.so;dl;m
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 F2003 interface DISABLED
Configuring NECI support:
-- Internal NECI ignored (source not available, run "/usr/bin/git submodule update --init /home/harper/OpenMolcas/External/NECI")
   An externally configured NECI can still be used
   Please use ExNEci command in your molcas input
EFP interface DISABLED
GEN1INT support DISABLED
libwfa 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: /home/harper/psi4conda/bin/cc
-- C compiler flags:  -std=gnu99 -O2
-- Fortran compiler: /home/harper/psi4conda/bin/gfortran
-- Fortran compiler flags:  -cpp -fno-aggressive-loop-optimizations -fdefault-integer-8 -O2
-- Definitions: _MOLCAS_;_I8_;_LINUX_
-- Debug definitions: 
-- pymolcas: added to targets
Definitions: -D_MOLCAS_;-D_I8_;-D_LINUX_
Configuring documentation
-- LaTeX compiler: /usr/bin/latexmk
-- Default documentation format: pdf
-- LaTeX HTML converter: /usr/bin/latex2html
Install directory: /opt/molcas
-- Configuring incomplete, errors occurred!
See also "/home/harper/build/CMakeFiles/CMakeOutput.log".

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