[Columbus] Installing Columbus with OpenMolcas
Zihan Pengmei
zpengmei at uchicago.edu
Tue Jun 7 15:47:15 EDT 2022
Hi Felix,
I followed the instructions, reinstalled the GA and redownload the code, the error is still there. I think the major problem is I don’t have those GA library files(libma, libglobal, libtcgmsg-mpi.a ) after building the GA package. I used the following command: ../configure MPICC=mpiicc CC=icc F77=ifort F90=ifort MPICXX=mpiicpc MPIF77=mpiifort MPIF90=mpiifort CXX=icpc --with-mpi=/software/intel/parallel_studio_xe_2018_update4/impi/2018.4.274 --with-ma --with-global --with-tcgmsg --with-tcgmsg-mpi --with-sockets --with-blas=-mkl --with-lapack=-mkl
Any suggestions?
Thanks,
Zihan
From: Zihan Pengmei <zpengmei at uchicago.edu>
Date: Tuesday, June 7, 2022 at 10:02 AM
To: columbus at lists.osc.edu <columbus at lists.osc.edu>
Subject: Re: Installing Columbus with OpenMolcas
Hi all,
Much appreciated for all of advice! I actually later found this problem and successfully compiled the sequential version, but failed at installing PARALLEL.
I built an OpenMolcas with intel_GA_mkl_mpi options and gave a keywork PMOLCAS with the route. Just to clarify, I am building a 7.0.2 source code, and the install.log.parallel warned it can’t find pciudg under source folder. Then, I copied this pciudg folder from 7.0 source code, but triggering the following error:
(it seems those GA libraries are still needed, but I didn’t find them anywhere in my GA build, is there any special flag that I should add when compiling?)
(Sorry for bothering on this, because I am running on cluster so it’s not easy to use precompiled 7.1 version.)
===== ./colinstall.sh: pciudg =====
/zpengmei/columbus/Columbus/makefile:22: INCFILE= /zpengmei/columbus/Columbus/machine.cfg/linux64.ifc
/zpengmei/columbus/Columbus/makefile:50: GAVERSION=GA58:
/zpengmei/columbus/Columbus/makefile:65: PMAKE= yes
/zpengmei/columbus/Columbus/makefile:69: setting DKEYWORDSLOCAL 1 to -DJSC -DUNIX -DLINUX -DMILSTD1753 -DBIT64 -DFORMATDOLLAR -DBLAS2 -DBLAS3 -DPIPEMODE -DF90 -DF95 -DINT64 -DMOLCAS_INT64 -DNOENVSUPPORT -DGA50 -DMOLCAS_LABEL10 -DPARALLEL -DMPI
/zpengmei/columbus/Columbus/makefile:70: setting CPPDIRLOCAL 1 to -I /zpengmei/columbus/Columbus/source/dalton/include -DCOLUMBUS -DSYS_LINUX -DPTR64 -Df90 -DVAR_BLAS3 -DINT64 -DPARALLEL -DMPI
/zpengmei/columbus/Columbus/makefile:81: setting DKEYWORDSLOCAL 3 to -DJSC -DUNIX -DLINUX -DMILSTD1753 -DBIT64 -DFORMATDOLLAR -DBLAS2 -DBLAS3 -DPIPEMODE -DF90 -DF95 -DINT64 -DMOLCAS_INT64 -DNOENVSUPPORT -DGA50 -DMOLCAS_LABEL10 -DPARALLEL -DMPI -DMOLCAS -DMOLCAS_INT64
/zpengmei/columbus/Columbus/makefile:82: LIBMOLCAS set to $LIBMOLCAS
/zpengmei/columbus/Columbus/makefile:85: PLIBS= /zpengmei/columbus/Columbus/libglobal.a /zpengmei/columbus/Columbus/libarmci.a /zpengmei/columbus/Columbus/libtcgmsg-mpi.a /zpengmei/columbus/Columbus/libma.a /software/intel/parallel_studio_xe_2018_update4/impi/2018.4.274/intel64/lib/libmpi.a
/zpengmei/columbus/Columbus/makefile:90: setting PLIBS to /zpengmei/columbus/Columbus/libglobal.a /zpengmei/columbus/Columbus/libarmci.a /zpengmei/columbus/Columbus/libtcgmsg-mpi.a /zpengmei/columbus/Columbus/libma.a /software/intel/parallel_studio_xe_2018_update4/impi/2018.4.274/intel64/lib/libmpi.a
/zpengmei/columbus/Columbus/makefile:91: setting LIBS to /zpengmei/columbus/Columbus/colib.a /zpengmei/columbus/Columbus/blaswrapper.a -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
/zpengmei/columbus/Columbus/makefile:92: setting LIBS2 to /zpengmei/columbus/Columbus/colib.a /zpengmei/columbus/Columbus/libmolcas_col.a /zpengmei/columbus/Columbus/blaswrapper.a -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
/zpengmei/columbus/Columbus/makefile:105: cpp WITH_REDIRECTON ::
$MPI_LD -o pciudg.x ciudg_data.o molcaswrapper.o ciudg_matutil.o ciudg_gautil.o ciudg_ioutil.o ciudg_drtutil.o ciudg_utils.o ciudg_loop.o ciudg_setup.o maksortmod.o cisrtmod.o ciudg_diag.o ciudg_allin.o ciudg_fourex_mod.o ciudg_threx.o ciudg_twoext.o ciudg_onext.o ciudg_allin.o ciudg_diag.o ciudg_spinorbit.o ciudg_oneden.o ciudg_twoden.o ciudg_main.o drivercid.o driver.o driversize.o driverwrap.o ciudg.o /zpengmei/columbus/Columbus/libdalton2.a /zpengmei/columbus/Columbus/libglobal.a /zpengmei/columbus/Columbus/libarmci.a /zpengmei/columbus/Columbus/libtcgmsg-mpi.a /zpengmei/columbus/Columbus/libma.a /software/intel/parallel_studio_xe_2018_update4/impi/2018.4.274/intel64/lib/libmpi.a -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl /zpengmei/columbus/Columbus/colib.a /zpengmei/columbus/Columbus/libmolcas_col.a /zpengmei/columbus/Columbus/blaswrapper.a -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl -Wl,--start-group /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_intel_ilp64.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_sequential.a /software/intel/parallel_studio_xe_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
gfortran: error: /zpengmei/columbus/Columbus/libglobal.a: No such file or directory
gfortran: error: /zpengmei/columbus/Columbus/libtcgmsg-mpi.a: No such file or directory
gfortran: error: /zpengmei/columbus/Columbus/libma.a: No such file or directory
gmake: *** [ /zpengmei/columbus/Columbus/makefile:388: pciudg.x] Error 1
+ for i in $*
+ cp pciudg.x /zpengmei/columbus/Columbus/pciudg.x
cp: cannot stat 'pciudg.x': No such file or directory
Much appreciated!
Zihan Pengmei
From: Columbus <columbus-bounces+zpengmei=uchicago.edu at lists.osc.edu> on behalf of columbus-request at lists.osc.edu <columbus-request at lists.osc.edu>
Date: Tuesday, June 7, 2022 at 9:18 AM
To: columbus at lists.osc.edu <columbus at lists.osc.edu>
Subject: Columbus Digest, Vol 112, Issue 2
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Today's Topics:
1. Re: Installing Columbus with OpenMolcas (Hans Lischka)
2. Re: Installing Columbus with OpenMolcas (Felix Plasser)
----------------------------------------------------------------------
Message: 1
Date: Mon, 6 Jun 2022 13:03:40 -0500
From: Hans Lischka <hans.lischka at univie.ac.at>
To: columbus at lists.osc.edu
Subject: Re: [Columbus] Installing Columbus with OpenMolcas
Message-ID: <a4fb80f2-4d90-0e3a-19db-59944b0ac590 at univie.ac.at>
Content-Type: text/plain; charset="UTF-8"; format=flowed
Hi Zihan,
Here is my interpretation of the problem:
The file libma.a is missing in the loading process (should be in
/zpengmei/columbus/Columbus/libma.a). This is GA library. You should
find this file (and two others, like libga.a and a third one) in the
libs directory of the GA installation. Copy them to the main Columbus
directory
Best regards, Hans
On 6/5/2022 9:35 PM, Zihan Pengmei via Columbus wrote:
> Dear Columbus developers, I am trying to compile a Columbus 7.0.2
> interfacing with openmolcas and sharc on the cluster(with intel
> compiler, mkl2020, intelmpi/2018.4), but having the following complaint:
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
>
> Dear Columbus developers,
>
> ??????????????? I am trying to compile a Columbus 7.0.2 interfacing
> with openmolcas and sharc on the cluster(with intel compiler, mkl2020,
> intelmpi/2018.4), but having the following complaint:
>
> e_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread
> -lm -ldl /zpengmei/columbus/Columbus/libma.a
>
> ifort: error #10236: File not found:'/zpengmei/columbus/Columbus/libma.a'
>
> gmake: *** [/zpengmei/columbus/Columbus/makefile:345: molcas.a] Error 1
>
> ??????????????? Just to clarify, I did git clone and compiled the
> openmolcas for columbus 7 from gitlab, one parallel version with
> intelmpi, mkl , intel compiler and ga 5.8.2, and another serial version
> with intel compiler, mkl.
>
> In install.config, I tried MOLCAS/PMOLCAS both keywords with
> corresponding versions, but neither of them worked out and came up with
> this warning when installing standard.
>
> ??????????????? I checked openmolcas/libs and ga/libs and I didn?t find
> libma.a anywhere. Any help would be very useful!
>
> Thanks,
>
> Zihan Pengmei
>
>
> _______________________________________________
> Columbus mailing list
> Columbus at lists.osc.edu
> https://lists.osu.edu/mailman/listinfo/columbus
------------------------------
Message: 2
Date: Tue, 7 Jun 2022 14:17:34 +0000
From: Felix Plasser <F.Plasser at lboro.ac.uk>
To: "columbus at lists.osc.edu" <columbus at lists.osc.edu>
Subject: Re: [Columbus] Installing Columbus with OpenMolcas
Message-ID: <0d3fc882-a1be-0890-4057-c315ab687fca at lboro.ac.uk>
Content-Type: text/plain; charset="utf-8"
Hi, I just remembered what this is. libma.a is only relevant for older
versions of Molcas. You can deactivate libma.a by setting in install.config:
VMOLCAS 8.0
But, in any case, I will make this the default. I don't think that
Columbus would be compatible with MOLCAS < 8 anyway ...
-Felix
On 06/06/2022 19:03, Hans Lischka 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. **
>
> Hi Zihan,
>
> Here is my interpretation of the problem:
> The file libma.a is missing in the loading process (should be in
> /zpengmei/columbus/Columbus/libma.a). This is GA library. You should
> find this file (and two others, like libga.a and a third one) in the
> libs directory of the GA installation. Copy them to the main Columbus
> directory
>
> Best regards, Hans
>
> On 6/5/2022 9:35 PM, Zihan Pengmei via Columbus wrote:
>> Dear Columbus developers, I am trying to compile a Columbus 7.0.2
>> interfacing with openmolcas and sharc on the cluster(with intel
>> compiler, mkl2020, intelmpi/2018.4), but having the following complaint:
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
>> ? ?
>>
>> Dear Columbus developers,
>>
>> ???????????????? I am trying to compile a Columbus 7.0.2 interfacing
>> with openmolcas and sharc on the cluster(with intel compiler, mkl2020,
>> intelmpi/2018.4), but having the following complaint:
>>
>> e_2020_update1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread
>> -lm -ldl /zpengmei/columbus/Columbus/libma.a
>>
>> ifort: error #10236: File not
>> found:'/zpengmei/columbus/Columbus/libma.a'
>>
>> gmake: *** [/zpengmei/columbus/Columbus/makefile:345: molcas.a] Error 1
>>
>> ???????????????? Just to clarify, I did git clone and compiled the
>> openmolcas for columbus 7 from gitlab, one parallel version with
>> intelmpi, mkl , intel compiler and ga 5.8.2, and another serial version
>> with intel compiler, mkl.
>>
>> In install.config, I tried MOLCAS/PMOLCAS both keywords with
>> corresponding versions, but neither of them worked out and came up with
>> this warning when installing standard.
>>
>> ???????????????? I checked openmolcas/libs and ga/libs and I didn?t find
>> libma.a anywhere. Any help would be very useful!
>>
>> Thanks,
>>
>> Zihan Pengmei
>>
>>
>> _______________________________________________
>> Columbus mailing list
>> Columbus at lists.osc.edu
>> https://lists.osu.edu/mailman/listinfo/columbus
>
> _______________________________________________
> Columbus mailing list
> Columbus at lists.osc.edu
> https://lists.osu.edu/mailman/listinfo/columbus
------------------------------
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