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#1 2021-04-12 10:03:36
- qling
- Member
- Registered: 2021-04-12
- Posts: 4
[SOLVED] Molcas Environment Setup
How to set the environment variable (MOLCAS) and Molcas driver (molcas)
export MOLCAS=/home/molcas/molcas.version
export PATH=$PATH:$HOME/bin
I followed the above step of Qiuckstart guide, and then run molcas xxx.input. It shows that "-bash: molcas: command not found".
What is the problem?
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#2 2021-04-12 10:21:24
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,202
Re: [SOLVED] Molcas Environment Setup
If you're using OpenMolcas, you should use "pymolcas" instead of "molcas", and you should copy it somewhere in you path (e.g. in $HOME/bin). See https://gitlab.com/Molcas/OpenMolcas/-/ … stallation
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#3 2021-04-12 13:41:01
- qling
- Member
- Registered: 2021-04-12
- Posts: 4
Re: [SOLVED] Molcas Environment Setup
Thanks. I am using Openmolcas and I can run molcas on my loading node now. However, I cannot submit the task to the queue by script.
The script is given as following:
#!/bin/sh
export PATH=$PATH:$HOME/molcas-build
export MOLCAS_NPROCS=2
bsub -q test -o %J.log -e %J.err python ~/molcas-build/pymolcas sew.input > sew.outputAnd the ouput is given:
/home/phys/ckduan2/molcas-build/bin/seward.exe: error while loading shared libraries: libhdf5.so.8: cannot open shared object file: No such file or directory
/home/phys/ckduan2/molcas-build/bin/seward.exe: error while loading shared libraries: libhdf5.so.8: cannot open shared object file: No such file or directory
cannot open file for reading: No such file or directory
0 parnell_reduce: cannot open source file rc.local
cannot open file for reading: No such file or directory
1 parnell_reduce: cannot open source file rc.local
0 parnell: ABORTING
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[cli_0]: readline failed
1 parnell: ABORTING
Abort(1) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
Traceback (most recent call last):
File "/home/phys/ckduan2/molcas-build/pymolcas", line 587, in <module>
sys.exit(main(os.path.realpath(f)))
File "<string>", line 217, in main
File "<string>", line 776, in auto
File "<string>", line 198, in run
File "<string>", line 346, in run
File "<string>", line 842, in run_module
File "<string>", line 1328, in run
File "<string>", line 1198, in _read_rc
File "<string>", line 75, in utf8_open
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/sew/rc.global'Can you give me some guidance, please? Thank you!
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#4 2021-04-12 14:34:36
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,202
Re: [SOLVED] Molcas Environment Setup
That is something the technical support of your HPC should help you with. Typically, though, your script should have something like:
#!/bin/sh
export PATH=$PATH:$HOME/molcas-build
export MOLCAS_NPROCS=2
~/molcas-build/pymolcas sew.input > sew.outputand then you submit the script with "bsub name_of_the_script". The specific error you're getting is about missing HDF5 libraries, you probably need to load the corresponding module inside the script too.
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#5 2021-04-14 03:34:26
- qling
- Member
- Registered: 2021-04-12
- Posts: 4
Re: [SOLVED] Molcas Environment Setup
I can successfully run the program now, thanks!
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#6 2026-05-19 14:08:54
- zushiwuxian
- Member
- Registered: 2026-05-19
- Posts: 2
Re: [SOLVED] Molcas Environment Setup
Hello, I am still getting the same error running with more than one MPI process, the following shows information related to my build:
Workstation is Intel(R) Xeon(R) CPU E5-2699 v4 with 2 socket Ubuntu 18.04.6 LTS 4.15.0-213-generic
How I built GA version 5.9.2:
```bash=
source /home/tempo/Bureau/intel/oneapi/setvars.sh
../configure \
CC=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiicc \
CXX=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiicpc \
F77=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiifort \
MPICC=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiicc \
MPICXX=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiicpc \
MPIF77=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiifort \
--prefix=/opt/ga592-ilp64-IntelMPI-tempo \
--enable-shared \
--enable-static \
--enable-i8 \
--with-mpi-pr \
--with-mpi=/home/tempo/Bureau/intel/oneapi/mpi/2021.5.1 \
--with-blas8="-L${MKLROOT}/lib -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
--with-scalapack8="-L${MKLROOT}/lib -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm" \
2>&1 |& tee c.log
```I built parallel hdf5 2.1.1
I built OpenMolcas using cmake-gui, here is the config log:
```bash
Configuring compilers:
Detecting Molcas version info:
-- OPENMOLCAS_VERSION: v26.02-460-g12f959d59-dirty
Detecting system info:
-- OS: Linux-x86_64
-- ADDRMODE: 64
-- PLATFORM: LINUX64
Configuring with MPI parallellization:
-- MPI_C_INCLUDE_PATH:
-- MPI_Fortran_INCLUDE_PATH:
-- MPI_C_LIBRARIES:
-- MPI_Fortran_LIBRARIES:
-- MPIEXEC: /home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiexec
-- MPI_IMPLEMENTATION: impi
Configuring HDF5 support:
Found HDF5: hdf5-shared (found version "2.1.1") found components: C
-- HDF5_INCLUDE_DIRS: /opt/hdf5/parallel/2.1.1/include
-- HDF5_C_LIBRARIES: hdf5-shared
Configuring linear algebra libraries:
-- Using Intel Math Kernel Library (MKL)
-- MKLROOT = /home/tempo/Bureau/intel/oneapi/mkl/2022.0.2
-- MKL_INCLUDE_PATH = /home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/include
-- MKL_LIBRARY_PATH = /home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib
-- LINALG_LIBRARIES: /home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_scalapack_ilp64.so;/home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_intel_ilp64.so;/home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_core.so;/home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_intel_thread.so;/home/tempo/Bureau/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_blacs_intelmpi_ilp64.so
Configuring Libxc:
-- Configuring built-in Libxc
-- Libxc_INCLUDE_DIRS: /opt/OpenMolcas/build-para-tempo/External/Libxc_install/include
-- Libxc_LIBRARIES: xcf03;xc
Configuring external Global Arrays library:
-> no libibverbs dependency found for GA.
-- GA_INCLUDE_PATH: /opt/ga592-ilp64-IntelMPI-tempo/include
-- GA_LIBRARIES: ga;armci
Gromacs interface DISABLED
BLOCK interface DISABLED
CHEMPS2 interface DISABLED
DICE interface DISABLED
MSYM support DISABLED
QCMaquis DMRG support DISABLED
NECI interface DISABLED
EFP interface DISABLED
GEN1INT support DISABLED
libwfa support DISABLED
NEVPT2 support DISABLED
MolGUI DISABLED
Configuring runtime environment settings:
-- DEFMOLCASMEM: 2048
-- DEFMOLCASDISK: 20000
-- RUNSCRIPT: $program $input
-- RUNBINARY: /home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiexec -n $MOLCAS_NPROCS $program
-- RUNBINARYSER: $program
Build type: Release
-- C compiler: /home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiicc
-- C compiler flags: -std=gnu99 -gcc-sys -qopenmp -O2
-- Fortran compiler: /home/tempo/Bureau/intel/oneapi/mpi/2021.5.1/bin/mpiifort
-- Fortran compiler flags: -fpp -i8 -heap-arrays -qopenmp -O2 -fno-alias -traceback
-- Definitions: _MOLCAS_;_I8_;_LINUX_;_MOLCAS_MPP_;_SCALAPACK_;_GA_
-- Debug definitions:
Configuring tools:
-- AugerOca: added to targets
-- CIsandbox: added to targets
-- Coord: ignored (no CMake support)
-- GA4GUGA: added to targets
-- analyze_molcas: ignored (no CMake support)
-- dynamixtools: added to targets
-- extra_tests: ignored (no CMake support)
-- format_basis: ignored (no CMake support)
-- grid2cube: added to targets
-- gridit: ignored (no CMake support)
-- hfc_converter: ignored (no CMake support)
-- job2asc: added to targets
-- mort: added to targets
-- patch2tinker: ignored (no CMake support)
-- pymolcas: added to targets
-- rf2asc: added to targets
-- rysroots: ignored (no CMake support)
-- syntax: ignored (no CMake support)
-- verify: ignored (no CMake support)
Definitions: -D_MOLCAS_;-D_I8_;-D_LINUX_;-D_MOLCAS_MPP_;-D_SCALAPACK_;-D_GA_
Configuring documentation
-- Sphinx compiler: no sphinx-build available, documentation disabled
Install directory: /opt/OpenMolcas-para-tempo
Configuring done (4.4s)
```So When I run the following script:
```bash
#!/bin/bash
export MOLCAS_PROJECT=test-prop_oxide
export MOLCAS_WORKDIR=/home/tempo/Bureau/test-openmolcas/work
export MOLCAS_MEM=10000
export MOLCAS_NPROCS=4
export MOLCAS_THREADS=1
export OMP_NUM_THREADS=1
mkdir -p "$MOLCAS_WORKDIR"
pymolcas -np $MOLCAS_NPROCS -nt $MOLCAS_THREADS prop_oxide.inp 2>&1 |& tee run.log
```I have the following log with parnell and rc.global error:
```bash
configuration info
------------------
Host name: wks-bohm (Linux)
C Compiler ID: Intel
C flags: -std=gnu99 -gcc-sys -qopenmp
Fortran Compiler ID: Intel
Fortran flags: -fpp -i8 -heap-arrays -qopenmp
Definitions: _MOLCAS_;_I8_;_LINUX_;_MOLCAS_MPP_;_SCALAPACK_;_GA_
Parallel: ON (GA=ON)
---------------------------------------------------------------------------
|
| Project: test-prop_oxide
| Submitted from: /home/tempo/Bureau/test-openmolcas
| Scratch area: /home/tempo/Bureau/test-openmolcas/work/test-prop_oxide
| Save outputs to: /home/tempo/Bureau/test-openmolcas
| Molcas: /opt/OpenMolcas-para-tempo
|
| Scratch area is empty (for the master process)
|
| MOLCAS_DRIVER = /opt/OpenMolcas-para-tempo/pymolcas
| MOLCAS_NPROCS = 4
| MOLCAS_SOURCE = /opt/OpenMolcas-para-tempo
| MOLCAS_STRUCTURE = 0
| MOLCAS_THREADS = 1
|
---------------------------------------------------------------------------
++ --------- Input file ---------
&GATEWAY
coord=prop_oxide.xyz
basis=aug-cc-pVDZ
group=C1
&SEWARD
&SCF
&RASSCF
nactel = 4 0 0
inactive= 0
ras2 = 5
ciroot = 5 5 1
-- ----------------------------------
--- Start Module: gateway at Tue May 19 14:43:42 2026 ---
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
&GATEWAY
launched 3 MPI processes, running in PARALLEL mode (work-sharing enabled)
available to each process: 10 GB of memory, 1 thread
master pid: 56050
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
++ Symmetry information:
---------------------
Character Table for C1
E
a 1 x, y, xy, Rz, z, xz, Ry, yz, Rx, I
--
++ Basis set information:
----------------------
Basis set label: C.AUG-CC-PVDZ.........
Electronic valence basis set:
------------------
Associated Effective Charge 6.000000 au
Associated Actual Charge 6.000000 au
Nuclear Model: Point charge
Shell nPrim nBasis Cartesian Spherical Contaminant
s 10 4 X
p 5 3 X
d 2 2 X
Basis set label: O.AUG-CC-PVDZ.........
Electronic valence basis set:
------------------
Associated Effective Charge 8.000000 au
Associated Actual Charge 8.000000 au
Nuclear Model: Point charge
Shell nPrim nBasis Cartesian Spherical Contaminant
s 10 4 X
p 5 3 X
d 2 2 X
Basis set label: H.AUG-CC-PVDZ.........
Electronic valence basis set:
------------------
Associated Effective Charge 1.000000 au
Associated Actual Charge 1.000000 au
Nuclear Model: Point charge
Shell nPrim nBasis Cartesian Spherical Contaminant
s 5 3 X
p 2 2 X
Basis set label: C.AUG-CC-PVDZ.........
Electronic valence basis set:
------------------
Associated Effective Charge 6.000000 au
Associated Actual Charge 6.000000 au
Nuclear Model: Point charge
Shell nPrim nBasis Cartesian Spherical Contaminant
s 10 4 X
p 5 3 X
d 2 2 X
Basis set label: H.AUG-CC-PVDZ.........
Electronic valence basis set:
------------------
Associated Effective Charge 1.000000 au
Associated Actual Charge 1.000000 au
Nuclear Model: Point charge
Shell nPrim nBasis Cartesian Spherical Contaminant
s 5 3 X
p 2 2 X
--
++ Molecular structure info:
-------------------------
************************************************
**** Cartesian Coordinates / bohr, angstrom ****
************************************************
Center Label x y z x y z
1 C1 -1.831655 -1.289126 -0.182469 -0.969270 -0.682176 -0.096558
2 C2 0.401785 -0.070215 0.925257 0.212615 -0.037156 0.489625
3 O3 -1.528723 1.403086 -0.289800 -0.808966 0.742481 -0.153356
4 H4 -1.657974 -2.258504 -1.987521 -0.877362 -1.195149 -1.051751
5 H5 -3.352646 -1.951396 1.031063 -1.774144 -1.032634 0.545615
6 H6 0.422583 0.160223 2.972073 0.223621 0.084786 1.572753
7 C7 2.954732 -0.119606 -0.329848 1.563577 -0.063293 -0.174548
8 H8 3.974587 1.641764 0.031917 2.103261 0.868784 0.016890
9 H9 4.094209 -1.682359 0.405396 2.166562 -0.890266 0.214526
10 H10 2.760695 -0.348493 -2.372686 1.460897 -0.184415 -1.255571
***************************************
* InterNuclear Distances / bohr *
***************************************
1 C1 2 C2 3 O3 4 H4 5 H5 6 H6
1 C1 0.000000
2 C2 2.775077 0.000000
3 O3 2.711326 2.715482 0.000000
4 H4 2.056228 4.185152 4.038094 0.000000
5 H5 2.055402 4.200689 4.040288 3.475353 0.000000
6 H6 4.139242 2.059851 3.999015 5.897162 4.741182 0.000000
7 C7 4.929402 2.845219 4.735142 5.347881 6.707500 4.170463
8 H8 6.507574 4.061262 5.517871 7.142546 8.221766 4.843162
9 H9 5.967921 4.062421 6.451406 6.256645 7.477934 4.843943
10 H10 5.174120 4.064274 5.079917 4.829196 7.178283 5.855937
7 C7 8 H8 9 H9 10 H10
7 C7 0.000000
8 H8 2.067220 0.000000
9 H9 2.069103 3.347176 0.000000
10 H10 2.064758 3.349145 3.357855 0.000000
*******************************************
* InterNuclear Distances / angstrom *
*******************************************
1 C1 2 C2 3 O3 4 H4 5 H5 6 H6
1 C1 0.000000
2 C2 1.468508 0.000000
3 O3 1.434772 1.436971 0.000000
4 H4 1.088109 2.214687 2.136867 0.000000
5 H5 1.087672 2.222909 2.138028 1.839078 0.000000
6 H6 2.190393 1.090026 2.116187 3.120644 2.508925 0.000000
7 C7 2.608527 1.505625 2.505729 2.829977 3.549456 2.206914
8 H8 3.443660 2.149127 2.919931 3.779673 4.350771 2.562891
9 H9 3.158088 2.149741 3.413937 3.310874 3.957152 2.563304
10 H10 2.738026 2.150721 2.688176 2.555500 3.798584 3.098829
7 C7 8 H8 9 H9 10 H10
7 C7 0.000000
8 H8 1.093926 0.000000
9 H9 1.094922 1.771249 0.000000
10 H10 1.092623 1.772291 1.776901 0.000000
**************************************
* Valence Bond Angles / degree *
**************************************
Atom centers Phi
2 C2 1 C1 3 O3 59.32
2 C2 1 C1 4 H4 119.31
2 C2 1 C1 5 H5 120.09
3 O3 1 C1 4 H4 115.08
3 O3 1 C1 5 H5 115.21
4 H4 1 C1 5 H5 115.40
1 C1 2 C2 3 O3 59.17
1 C1 2 C2 6 H6 116.99
1 C1 2 C2 7 C7 122.58
3 O3 2 C2 6 H6 113.02
3 O3 2 C2 7 C7 116.74
6 H6 2 C2 7 C7 115.54
1 C1 3 O3 2 C2 61.51
2 C2 7 C7 8 H8 110.53
2 C2 7 C7 9 H9 110.52
2 C2 7 C7 10 H10 110.74
8 H8 7 C7 9 H9 108.04
8 H8 7 C7 10 H10 108.30
9 H9 7 C7 10 H10 108.64
***************************************************************
* Valence Dihedral Angles / degree *
***************************************************************
Atom centers Phi1 Phi2 Theta
3 O3 1 C1 2 C2 6 H6 59.32 116.99 101.95
3 O3 1 C1 2 C2 7 C7 59.32 122.58 -103.91
4 H4 1 C1 2 C2 6 H6 119.31 116.99 -154.62
4 H4 1 C1 2 C2 7 C7 119.31 122.58 -0.49
5 H5 1 C1 2 C2 6 H6 120.09 116.99 -1.26
5 H5 1 C1 2 C2 7 C7 120.09 122.58 152.87
3 O3 2 C2 1 C1 4 H4 59.17 119.31 103.43
3 O3 2 C2 1 C1 5 H5 59.17 120.09 -103.22
1 C1 2 C2 7 C7 8 H8 122.58 110.53 145.75
1 C1 2 C2 7 C7 9 H9 122.58 110.52 -94.70
1 C1 2 C2 7 C7 10 H10 122.58 110.74 25.74
3 O3 2 C2 7 C7 8 H8 116.74 110.53 76.80
3 O3 2 C2 7 C7 9 H9 116.74 110.52 -163.65
3 O3 2 C2 7 C7 10 H10 116.74 110.74 -43.22
6 H6 2 C2 7 C7 8 H8 115.54 110.53 -59.77
6 H6 2 C2 7 C7 9 H9 115.54 110.52 59.78
6 H6 2 C2 7 C7 10 H10 115.54 110.74 -179.78
2 C2 3 O3 1 C1 4 H4 61.51 115.08 -110.53
2 C2 3 O3 1 C1 5 H5 61.51 115.21 111.41
1 C1 3 O3 2 C2 6 H6 61.51 113.02 -108.71
1 C1 3 O3 2 C2 7 C7 61.51 116.74 113.67
--
Nuclear Potential Energy 124.46283269 au
cannot open file for reading: No such file or directory
3 parnell_reduce: cannot open source file rc.local
0 parnell: ABORTING
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
1 parnell: ABORTING
Abort(1) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
2 parnell: ABORTING
Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
3 parnell: ABORTING
Abort(1) on node 3 (rank 3 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
.########################.
.# Non-zero return code #.
.########################.
Aborting...
Traceback (most recent call last):
File "/opt/OpenMolcas-para-tempo/pymolcas", line 601, in <module>
sys.exit(main(os.path.realpath(f)))
File "<string>", line 221, in main
File "<string>", line 784, in auto
File "<string>", line 198, in run
File "<string>", line 346, in run
File "<string>", line 848, in run_module
File "<string>", line 1361, in run
File "<string>", line 1208, in _read_rc
File "<string>", line 75, in utf8_open
FileNotFoundError: [Errno 2] No such file or directory: '/home/tempo/Bureau/test-openmolcas/work/test-prop_oxide/rc.global'
```Offline
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