[CP2K-user] [CP2K:19617] graph compilation
Krack Matthias
matthias.krack at psi.ch
Fri Dec 1 14:42:15 UTC 2023
Dear Victor
1. The typical CPU and memory resources of a Windows PC usually do not allow for running several CP2K jobs concurrently and the installation of a job scheduler like slurm (if possible) might not be worth the effort. Alternatively, one can use the Linux shell feature for sending jobs into the background by appending “&” to the command. I have added some further hints to the wiki page how to launch a parallel run with mpiexec, hth.
2. I cannot assess if your assignment of the processes is correct. I suggest to run only the cp2k.sopt and cp2k.popt binaries. If you launch just cp2k.ssmp, it will start by default 12 threads on a Windows PC with a 6-core CPU and hyperthreading which will be quite inefficient.
Best
Matthias
From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Victor Volkov <volkovskr at gmail.com>
Date: Friday, 1 December 2023 at 13:03
To: cp2k at googlegroups.com <cp2k at googlegroups.com>
Subject: Re: [CP2K:19618] graph compilation
Two issues:
1)
a chemistry student might need a short hint that it is possible to run several CP2K jobs on the same computer simultaneously
and how to do this
2)
I have noticed that WSL-Ubuntu local installation runs the same job 6-times faster than when under Sygwin.
At the same time (I would need to reconfirm this), Task Manager shows Vmmem (I think this is the WSL-Ubuntu util by cp2k) takes 6 times
more intense usage of CPU. This is a curious. difference - I attach an image.
Victor
On Fri, Dec 1, 2023 at 12:37 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Dear Victor
I am glad that you could finally get graph work on your local Windows PC.
I have further extended the How to Compile CP2K on Windows<https://www.cp2k.org/howto:compile_on_windows> with the instructions to build also an MPI/OpenMP parallel CP2K (psmp) binary under Windows and with some further information and hints. The cp2k.psmp binary will provide better performance in case you have a larger number of CPU cores (more than 4) available.
Best
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Thursday, 30 November 2023 at 13:34
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19604] graph compilation
Dear Mathias:
thank you for the kind reply with instructions.
I cd into
/github/cp2k/cp2k/exe/local/
and instructed
./cp2k.ssmp -v
The package printed its version and command format properly.
Then, I copied into the same directory the files I generated while
following the Metadynamics tutorial
https://www.cp2k.org/howto:biochem_qmmm
and I edited the instruction from the tutorial as
./graph.ssmp -cp2k -file METADYN-1.restart -out fes.dat
In return, the package started to print:
**********************************************************************
FES| Parsing file: <METADYN-1.restart>
**********************************************************************
FES| Parameters for FES:
FES| NDIM :: 1
etc.
....
and after few minutes
the package produced the fes.dat file.
Therefore, the proper performance of graph routing is confirmed.
Thank you, dear Matthias!
Now, I understand how to approach and elaborate the usage of it further.
:-)
With best regards,
Victor
On Thu, Nov 30, 2023 at 2:15 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Dear Victor
Thanks for testing.
After running
make -j ARCH=local VERSION=ssmp
in “~/github/cp2k/cp2k/”
there should already be a “graph.ssmp” binary
in “~/github/cp2k/cp2k/exe/local/”
Is that the case and can you run
~/github/cp2k/cp2k/exe/local/cp2k.ssmp -v
and/or
~/github/cp2k/cp2k/exe/local/graph.ssmp
?
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Thursday, 30 November 2023 at 09:14
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19598] graph compilation
Dear Matthias:
good morning.
local installation is running properly
CP2K| version string: CP2K version 2023.2 (Development Version)
CP2K| source code revision number: git:845a3ae
Considering the given format to install
make -j ARCH=local VERSION=ssmp
I cd into
github/cp2k/cp2k
and tried to compile graph instructing
make ARCH=local VERSION=ssmp fes
The package returned
*******************************
Discovering programs ...
Removing stale archives for ssmp ...
Resolving dependencies for ssmp ...
make -C /home/volkovskr/github/cp2k/cp2k/exts/dbcsr -f /home/volkovskr/github/cp2k/cp2k/exts/build_dbcsr/Makefile \
ARCHFILE=/home/volkovskr/github/cp2k/cp2k/arch/local.ssmp \
LIBDIR=/home/volkovskr/github/cp2k/cp2k/lib/local/ssmp/exts/dbcsr \
OBJDIR=/home/volkovskr/github/cp2k/cp2k/obj/local/ssmp/exts/dbcsr \
USE_ACCEL="" \
ACC="" \
ACCFLAGS=""
Removing stale archives ...
Resolving dependencies ...
********************************
However,
there is no any outcome:
content of the folder
github/cp2k/cp2k/local
is the same as before.
There is graph.ssmp file there with its time creation when CP2K version 2023.2was compiled.
It seems, under WLS, compiling graph is the same problematic as under Cygwin.
I anticipate that graph-fes protocol is not your product.
May be it could be possible to post this to the author.
Thank you.
With best regards.
Victor
On Wed, Nov 29, 2023 at 8:29 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Dear Victor
I just created a small howto<https://www.cp2k.org/howto:compile_on_windows> for the installation of CP2K under Windows using the Windows System for Linux (WSL).
I will check this evening that howto on my old Win10 office PC at home, but any other tests are appreciated. I am pretty sure that there are at least some typos. This should also provide the “fes” (graph.ssmp) tool under Windows.
HTH
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Sunday, 26 November 2023 at 14:21
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19574] graph compilation
> Did you consider instead of installing and using CP2K with Cygwin<https://www.cp2k.org/howto:compile_on_windows_with_cygwin> to use a Windows Subsystem for Linux (WSL) as suggested?
Dear Matthias:
I was working to try to install CP2K under WLS ubuntu.
The standard protocol
using
git clone --recursive https://github.com/cp2k/cp2k.git cp2k
make ARCH=Darwin-gfortran VERSION=sopt
does not work - the installer is not universal: it cannot find directories, it cannot find gfortran.
(Comparatively, miniconda and amber-tools are universal.)
However, on YouTube there is a description
to do
sudo apt install cp2k.
This does work, but it installs the retired version 6.1
and it is not clear where its location, neither how to deal with it.
Curiously, ubuntu tells that (wherever it is) it is popt.
I never was able to compile popt under Cygwin.
Somewhere on pc there is this cp2k.popt package, but it is not clear
if this can be used to generate graph and how.
I will explore this: even the outdated dummy soft, still it might help to plot FES
:-)
Best,
Victor
On Tue, Nov 21, 2023 at 12:49 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Dear Victor
Did you consider instead of installing and using CP2K with Cygwin<https://www.cp2k.org/howto:compile_on_windows_with_cygwin> to use a Windows Subsystem for Linux (WSL) as suggested?
Best
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Tuesday, 21 November 2023 at 09:40
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19535] graph compilation
Dear Mattheas:
while still trying to make fes,
I managed to get this response
$ make ARCH=Cygwin-x86_64-gfortran VERSION=sopt fes
Discovering programs ...
Version sopt is now an alias for ssmp with OMP_NUM_THREADS=1.
Removing stale archives for ssmp ...
Resolving dependencies for ssmp ...
make -C /cp2k2023/cp2k/exts/dbcsr -f /cp2k2023/cp2k/exts/build_dbcsr/Makefile \
ARCHFILE=/cp2k2023/cp2k/arch/Cygwin-x86_64-gfortran.ssmp \
LIBDIR=/cp2k2023/cp2k/lib/Cygwin-x86_64-gfortran/ssmp/exts/dbcsr \
OBJDIR=/cp2k2023/cp2k/obj/Cygwin-x86_64-gfortran/ssmp/exts/dbcsr \
USE_ACCEL="" \
ACC="" \
ACCFLAGS=""
Removing stale archives ...
Resolving dependencies ...
However,
I do not find any executable to be generated neither in
cp2k\exe\Cygwin-x86_64-gfortran
nor in
cp2k\exe
May be something is inconsistent about the ssmp file - below I provide its content.
Would you give a hint?
Thank you.
Victor
**************
CC = gcc
CPP =
AR = ar -r
FC = gfortran -fopenmp
LD = gfortran -fopenmp
CFLAGS = -fopenmp -funroll-loops -ftree-vectorize -march=native -mtune=native
DFLAGS = -D__GFORTRAN -D__FFTW3 -D__LIBINT -D__LIBXC -fopenmp
FCFLAGS = -g -O2 -funroll-loops -ftree-vectorize -march=native -ffree-form $(DFLAGS) -fopenmp
FCFLAGS = -ffree-form -ffree-line-length-none -fno-omit-frame-pointer
FCFLAGS += -I/usr/include -I/usr/local/include -I/libint-v2.6.0-cp2k-lmax-7/include
FCFLAGS += -fbacktrace -std=f2008 -Wl,--stack,4194304
LDFLAGS = $(FCFLAGS)
LIBS = -llapack -lblas -lint2 -lxc -lxcf03 -ldl -ldbghelp -lstdc++
LIBS += -lgsl -lz -ldl -lm -fopenmp -fopenmp-simd
LIBS += -L/usr/local/lib
LIBS += /lib/gcc/x86_64-pc-cygwin/7.4.0/libstdc++.a
LIBS += /lib/gcc/x86_64-pc-cygwin/7.4.0/libgomp.dll.a
LIBS += /lib/libgsl.dll.a /lib/libmpi.dll.a
LIBS += /lib/liblapack.dll.a /lib/libblas.dll.a /lib/libhdf5.dll.a /lib/libhdf5_hl.dll.a
LIBS += /lib/libfftw3.dll.a /lib/libfftw3_omp.dll.a /lib/libfftw3_threads.dll.a -llapack -lblas
LIBS += /lib/libfftw3f.dll.a /lib/libfftw3f_omp.dll.a /lib/libfftw3f_threads.dll.a
LIBS += /lib/libfftw3l.dll.a /lib/libfftw3l_omp.dll.a /lib/libfftw3l_threads.dll.a
LIBS += /usr/local/lib/libint2.a /usr/local/lib/libfftw3.a /usr/local/lib/libfftw3_threads.a
LIBS += /usr/local/lib/libxc.a /usr/local/lib/libxcf03.a /usr/local/lib/libxcf90.a
OBJECTS_ARCHITECTURE = machine_gfortran.o
On Thu, Jul 6, 2023 at 8:29 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
That should work, Victor. No clue, why it doesn’t create graph.<VERSION>.
Do you have any file in exe/Linux…/ ?
Does
make ARCH=Linux-x86-64-gfortran VERSION=sopt execlean
make ARCH=Linux-x86-64-gfortran VERSION=sopt fes
trigger any compiler/linker output?
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Thursday, 6 July 2023 at 19:18
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19070] graph compilation
This runs make, indeed,
but it seems an idle run:
I do not see neither fes.sopt nor graph.sopt
to be generated in the exe directory.
:-)
Victor
On Thu, Jul 6, 2023 at 7:59 PM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Dear Victor
Try just
make ARCH=Linux-x86-64-gfortran VERSION=sopt fes
HTH
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Thursday, 6 July 2023 at 18:46
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: Re: [CP2K:19069] graph compilation
Dear Matthias:
good evening.
Sorry to bother in the graph compilation.
Having the CP2K response, as I copy below,
what should I add to the arch file
...
or something else?
Thank you.
Best,
Victor
$ make fes.sopt ARCH=Linux-x86-64-gfortran VERSION=sopt
Discovering programs ...
make: *** No rule to make target 'fes.sopt'. Stop.
On Wed, Jun 28, 2023 at 10:22 AM Krack Matthias <matthias.krack at psi.ch<mailto:matthias.krack at psi.ch>> wrote:
Hi Victor
The binary graph.<VERSION> is created by default when CP2K is built. So, you should find it after a successful CP2K build in the folder cp2k/exe/<ARCH>/ where also the cp2k binary is stored. You can create it selectively via the make target “fes”, e.g. by “make ARCH=… VERSION=… fes”.
HTH
Matthias
From: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Victor Volkov <volkovskr at gmail.com<mailto:volkovskr at gmail.com>>
Date: Tuesday, 27 June 2023 at 21:14
To: cp2k <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>>
Subject: [CP2K:18999] graph compilation
Dear developers:
sorry to bother.
CP2K instructs that graph.sopt should be compiled on its own.
I found three F-files on git, and copied them
and placed into created graph directory.
When I tried to use gfortran, it started but with errors: please, see below.
If possible, would you hint how to compile this tool?
I run under both, Cygwin and WLS-Ubuntu.
Thank you.
Victor
gfortran graph.f -o graph.sopt
graph.f:18:1:
PROGRAM graph
1
Error: Non-numeric character in statement label at (1)
graph.f:18:1:
PROGRAM graph
1
Error: Unclassifiable statement at (1)
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