[Columbus] COLUMBUS-MOLCAS link
Kalpa Dihingia
20jyotikalpa15 at gmail.com
Tue Aug 8 08:43:08 EDT 2023
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
On Tue, Aug 8, 2023 at 5:47 PM Rene F. K. Spada <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> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Aug 8, 2023 at 4:17 PM Felix Plasser <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!2YKrXWz3zpUAh7ZhF4DDjVXB6o1Ll1f-MxK4Kx-H7f_IeJPPUYW0f1AXCLmHvMveNACTJmGyua1cKuSlNnGSzUfcrO-G$
>>> <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: image.png]
>>>
>>> *./install.automatic -p linux64.ifc standard grad parallel *
>>> [image: image.png]
>>>
>>> [image: image.png]
>>>
>>>
>>>
>>>
>>> *Thank you !*
>>>
>>> Kalpajyoti Dihingia
>>> Research Scholar,
>>> Department of Chemistry,
>>> Institute of Science,
>>> Banaras Hindu University, Varanasi-221005
>>> Phone no: 7576867088, 9707836598
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Columbus mailing listColumbus at lists.osc.eduhttps://lists.osu.edu/mailman/listinfo/columbus
>>>
>>> _______________________________________________
>> Columbus mailing list
>> Columbus at lists.osc.edu
>> https://lists.osu.edu/mailman/listinfo/columbus
>>
>
>
> --
>
>
> *Rene Felipe Keidel SpadaFísico por Formação, Humano por Natureza*
> *Instituto Tecnológico de Aeronáutica*
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 209858 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 308640 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 450072 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: install.config
Type: application/octet-stream
Size: 1160 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0003.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: install.log.cpan
Type: application/octet-stream
Size: 249 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0004.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: install.log.standard
Type: application/octet-stream
Size: 40606 bytes
Desc: not available
URL: <http://lists.osu.edu/pipermail/columbus/attachments/20230808/0486d02a/attachment-0005.obj>
More information about the Columbus
mailing list