[Columbus] COLUMBUS-MOLCAS link
Felix Plasser
F.Plasser at lboro.ac.uk
Tue Aug 8 10:56:14 EDT 2023
ok! So, the first thing to do is to get the source release
wget https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus-web/releases/Col7.2_2022-09-23_linux64.ifc_src.tar.gz__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9iXZs1EwQ$
Then you can work your way up. I would start with the basic installation and then include the parallel parts and OpenMolcas.
See the following pages
https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus/installation.html__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9iqKFpe7k$
https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus/parallel/parallel_general.html__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9iXuBXO4E$
https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus/columbus_molcas_link.html__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9igILbcMs$
None of this is particularly straightforward, sorry. But it is possible ...
On 08/08/2023 15:38, Kalpa Dihingia wrote:
** THIS MESSAGE ORIGINATED OUTSIDE LOUGHBOROUGH UNIVERSITY **
** Be wary of links or attachments, especially if the email is unsolicited or you don't recognise the sender's email address. **
I downloaded the precompiled executables using wget https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus-web/releases/Col7.2_2022-09-23_linux64.ifc_bin.tar.gz__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9iRnqL_HE$
Thank you !
Kalpajyoti Dihingia
Research Scholar,
Department of Chemistry,
Institute of Science,
Banaras Hindu University, Varanasi-221005
Phone no: 7576867088, 9707836598
[https://urldefense.com/v3/__https://ci3.googleusercontent.com/mail-sig/AIorK4wmJojwZSEvltXP7H1i_h0YEv6U0Fbyjua75Q3ZEsFhfEHsIE5V7ias_icyETQFdCCNi1p0D1M__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9ic3tPTss$ ]
On Tue, Aug 8, 2023 at 8:03 PM Felix Plasser <F.Plasser at lboro.ac.uk<mailto:F.Plasser at lboro.ac.uk>> wrote:
The first error is
/opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus/source/dalton2: No such file or directory
Did you download the source code or the precompiled executables?
On 08/08/2023 13:43, Kalpa Dihingia wrote:
** THIS MESSAGE ORIGINATED OUTSIDE LOUGHBOROUGH UNIVERSITY **
** Be wary of links or attachments, especially if the email is unsolicited or you don't recognise the sender's email address. **
Thank you Dr Rene for your kind response.
I have just removed the perl line from install.config and ran the following 2 lines (for trial) logging as a user
./install.automatic -p linux64.ifc cpan standard grad parallel
./install.automatic -p linux64.ifc standard grad parallel
And got the same error:
[kalpa at compute Col7.2_2022-09-23_linux64_parallel]$ ./install.automatic -p linux64.ifc cpan standard grad parallel
install.automatic bash version 09/2022 (fp)
install will not extract the source code, hence it must have been extracted before
packageid CPAN
packageid STANDARD
packageid GRAD
packageid PARALLEL
--> COMPRESS
Using $COLUMBUS/colperl as perl interpreter
============================
settings : CPPL = cpp -E -traditional
: PERL = /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus/colperl
: RANLIB = /usr/bin/ranlib
: GMAKE = gmake
: GREP = /bin/grep
: TAR = /bin/tar
: GUNZIP = /bin/gunzip
: BLASLIBRARY = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
: LAPACKLIBRARY = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
: COLUMBUS = /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus
: DALTON = /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus/source/dalton
: DALTON2 =
: GACOMMUNICATION = MPI
: MPI_MAINDIR = /opt/compilers/mpich/3.4.3
: MPI_LIBS = /opt/compilers/mpich/3.4.3/lib/libmpich.a
: MPI_STARTUP = /opt/compilers/mpich/3.4.3/bin/mpirun -np _NPROC_ _EXE_ _EXEOPTS_
: PSCRIPT =
: MPI_FC = /opt/compilers/mpich/3.4.3/bin/mpif90 -Wl -z muldefs
: MPI_LD = /opt/compilers/mpich/3.4.3/bin/mpif90 -Wl, -z muldefs
: MPI_CC = /opt/compilers/mpich/3.4.3/bin/mpicc
: MOLCAS = /opt/SOFTWARES/openmolcas/parallel_Mlcs
: VMOLCAS =
: PMOLCAS =
: MCFLAGS =
: INSTALLOPTION = NOGA_INSTALL
: COLUMBUSVERSION = 7.2
: GAVERSION = GA53
============================
---------- configuration file Columbus/machine.cfg/linux64.ifc ------------------
FORTRAN=ifort -c -nowarn -mkl=sequential
FFLAGS= -i8 -O2
FFLAGSCARE= -i8 -O0 -g -noautomatic
FFLAGS2= -i8 -O2 -noautomatic
CFLAGS= -DLINUX -DBIT64 -DINT64
CXX=icpc -c
CC=gcc -c -O $(CFLAGS)
CCMOLDEN=gcc -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
LOADER=ifort -z muldefs
MOLDENLIBS= -L/usr/X11R6/lib -lX11 -lm
AR=ar rv
ARX=ar x
CPPDIR=-I$(DALTON_DIR)/include -DCOLUMBUS -DSYS_LINUX -DPTR64 -Df90 -DVAR_BLAS3 -DINT64
SPEC=$(COLUMBUS)/special/UNIX
KOPC=$(SPEC)/fdate.c $(SPEC)/fwtime.c $(SPEC)/hostnm.c \
$(SPEC)/flushstdout.c $(SPEC)/fsize.c $(SPEC)/getputvec.c $(SPEC)/workdir.c
CDEF=icc -c -DFLUSH -DINT64 -DEXTNAME -I$(SPEC)
YES=1
FIXED=-fixed
FREE=-free
OBJECTSCARE=mcscf8.o gdiis.o givens.o suscal.o transmo.o polyhes.o utilities.o dzero.o
OBJECTSCAREFREE= ciudg_loop.o potentialmodfree.o potenrg.o
BLASCONVERSION=StoDblas
KEYWORDS=jsc:unix:linux:milstd1753:bit64:format:blas2:blas3:pipemode:f90:f95:int64:molcas_int64:noenvsupport:shavittgraph:ga50:molcas_label10
DKEYWORDS=-DJSC -DUNIX -DLINUX -DMILSTD1753 -DBIT64 -DFORMATDOLLAR -DBLAS2 -DBLAS3 -DPIPEMODE -DF90 -DF95 -DINT64 -DMOLCAS_INT64 -DNOENVSUPPORT -DGA50 -DMOLCAS_LABEL10
DALTON2CPP=-DRCLU4 -DVAR_IFC -DSYS_LINUX -D_FILE_OFFSET_BITS=64 -DVAR_MFDS -DIMPLICIT_NONE
MOLCASFF=$(FFLAGS)
PARALLELKEYS=parallel:mpi
DPARALLELKEYS=-DPARALLEL -DMPI
MOLCASKEYS=molcas:molcas_int64
DMOLCASKEYS=-DMOLCAS -DMOLCAS_INT64
STATIC=-static -static-libgcc
------------------------------------------------------------------------
cpan.tar /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/install.log.cpan
starting installation of cpan package
path= /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus
Starting colperl CPAN installation ...
cpan package installation successful
standard.tar /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/install.log.standard
starting installation of standard package
path= /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus
cp: cannot stat ‘/opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus/source/potential/pot_reduce.py’: No such file or directory
installation of standard package failed
check /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/install.log.standard for details
[kalpa at compute Col7.2_2022-09-23_linux64_parallel]$
Please look at the files attached.
Thank you !
Kalpajyoti Dihingia
Research Scholar,
Department of Chemistry,
Institute of Science,
Banaras Hindu University, Varanasi-221005
Phone no: 7576867088, 9707836598
[https://urldefense.com/v3/__https://ci3.googleusercontent.com/mail-sig/AIorK4wmJojwZSEvltXP7H1i_h0YEv6U0Fbyjua75Q3ZEsFhfEHsIE5V7ias_icyETQFdCCNi1p0D1M__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9ic3tPTss$ ]
On Tue, Aug 8, 2023 at 5:47 PM Rene F. K. Spada <rfkspada at gmail.com<mailto:rfkspada at gmail.com>> wrote:
Hi Kalpa,
You are having a lot of errors related to perl.
"Can't locate Shell.pm in @INC (you may need to install the Shell module) (@INC entries checked: /root/perl5/lib/perl5 /opt/compilers/perl/5.38/lib/site_perl/5.38.0/x86_64-linux /opt/compilers/perl/5.38/lib/site_perl/5.38.0 /opt/compilers/perl/5.38/lib/5.38.0/x86_64-linux /opt/compilers/perl/5.38/lib/5.38.0) at /opt/SOFTWARES/COLUMBUS/Col7.2_2022-09-23_linux64_parallel/Columbus/StoDblas line 8."
I believe you can remove the PERL variable from your install.config file. This will make Columbus use colperl. Could you test it?
I see from the screenshots that you are trying to install it as root. I would also suggest installing it as a user, not as root.
I believe these hints won't solve your problem but would make then a better.
Best,
Em ter., 8 de ago. de 2023 às 07:57, Kalpa Dihingia via Columbus <columbus at lists.osc.edu<mailto:columbus at lists.osc.edu>> escreveu:
Sure, sir Here I have attached the files. Thank you ! Kalpajyoti Dihingia Research Scholar, Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005 Phone no: 7576867088, 9707836598On Tue, Aug 8, 2023 at 4: 17
Sure, sir
Here I have attached the files.
Thank you !
Kalpajyoti Dihingia
Research Scholar,
Department of Chemistry,
Institute of Science,
Banaras Hindu University, Varanasi-221005
Phone no: 7576867088, 9707836598
[https://urldefense.com/v3/__https://ci3.googleusercontent.com/mail-sig/AIorK4wmJojwZSEvltXP7H1i_h0YEv6U0Fbyjua75Q3ZEsFhfEHsIE5V7ias_icyETQFdCCNi1p0D1M__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9ic3tPTss$ ]
On Tue, Aug 8, 2023 at 4:17 PM Felix Plasser <F.Plasser at lboro.ac.uk<mailto:F.Plasser at lboro.ac.uk>> wrote:
Hi Kalpa,
The OpenMolcas interface can be a bit tricky. If you attach, the install.config and install.log.standard files, then I can have a look. I can't actually read those screenshots you sent ...
-Felix
On 08/08/2023 09:16, Kalpa Dihingia via Columbus wrote:
** THIS MESSAGE ORIGINATED OUTSIDE LOUGHBOROUGH UNIVERSITY **
** Be wary of links or attachments, especially if the email is unsolicited or you don't recognise the sender's email address. **
Dear Columbus development team I am working with both columbus and OpenMolcas quantum chemistry software. But OpenMolcas is limited to RASSCF and CASPT2 level of theory, that is why I want to interface between both the softwares (both of calling
Dear Columbus development team
I am working with both columbus and OpenMolcas quantum chemistry software. But OpenMolcas is limited to RASSCF and CASPT2 level of theory, that is why I want to interface between both the softwares (both of calling OpenMolcas from columbus and Columbus from OpenMolcas).
I downloaded Columbus using: wget https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus-web/releases/Col7.2_2022-09-23_linux64.ifc_bin.tar.gz__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9iRnqL_HE$ <https://urldefense.com/v3/__https://columbus-program-system.gitlab.io/columbus-web/releases/Col7.2_2022-09-23_linux64.ifc_bin.tar.gz__;!!KGKeukY!xDHZY9lud6MjdKeAaC-sQ5olmflWmQdXzgQoqKKtirVJYrBEvRfttWBkKA28piMH08rWhs5zkh80_eZQkxh86z5hCjX2$>
I followed the columbus documentation but was not able to compile it properly. Can anyone please let me know how to solve this problem
I did the following:
Step 1: Edited the install.config:
[image.png]
./install.automatic -p linux64.ifc standard grad parallel
[image.png]
[image.png]
Thank you !
Kalpajyoti Dihingia
Research Scholar,
Department of Chemistry,
Institute of Science,
Banaras Hindu University, Varanasi-221005
Phone no: 7576867088, 9707836598
[https://urldefense.com/v3/__https://ci3.googleusercontent.com/mail-sig/AIorK4wmJojwZSEvltXP7H1i_h0YEv6U0Fbyjua75Q3ZEsFhfEHsIE5V7ias_icyETQFdCCNi1p0D1M__;!!KGKeukY!yrPi_royWKJL52d4yiRDvRL_9MLYEdYwPFptbNN-4Z1WiZVeaCbIb1weOd3b_N84Qa_n4HElGzrINmUdvB9ic3tPTss$ ]
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Rene Felipe Keidel Spada
Físico por Formação, Humano por Natureza
Instituto Tecnológico de Aeronáutica
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