[CP2K-user] [CP2K:19616] graph compilation

Krack Matthias matthias.krack at psi.ch
Fri Dec 1 14:27:23 UTC 2023
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Dear Victor

Thanks for the feedback.
I did not need a PowerShell for the WSL installation. No clue, if it is used In the background, because it is installed.
Anyway, I just clicked in the browser on the install button shown in the Microsoft Store for the App Ubuntu 22.04.2 LTS and a terminal window opens requesting username and password, done. That’s as easy as installing an App on the Smartphone. For convenience, I pinned that App also to the task bar by dragging the icon there.

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 12:41
To: cp2k at googlegroups.com <cp2k at googlegroups.com>
Subject: Re: [CP2K:19617] graph compilation
Excellent, dear Matthias:
I have 6 cores (12 logical processors).
According to your notice, it may be interesting to explore setting up a popt version.

In PS, I provide a description I developed while working on WSL-Ubuntu installation.

I think, CP2K is seriously "under-selling" its capacity among students and postdocs
world-wide.
Potentially, there is a several million community if they see how easy to install,
and how easy to follow examples.

Just watching what kind of demos people prepare to sell self on YouTube while using CP2K,
it seems to me that CP2K misses the huge market of students in Asia/Africa/America.

G16 is expensive, QChem and Turbomole and VASP are not cheap, Quantum Espresso is not handy at all
and their "discussion group" is below any level, Crystal is underdeveloped, Dalton is sort of "narrow" and underdeveloped,
CPMD is dragging behind slow.

Perhaps, only ABINIT may be a competitor, but their installation is not described,
and their discussion group and archive are not competitive.
They do demonstrate an amazing database of Raman examples
https://www.wurm.info/

I do believe that CP2K may have an EXPANSE.
Within the past 20 years, the world-wide experimental chemistry-bio-phys community of students and postdocs did grow up to start to pick
theoretical tools if hints to compile.

I can see this, since I remember black-white Norton Commander and a hard-drive of 20 MB.

With best regards,
Victor

PS:
In order to install Ubuntu in Windows environment,
you would need to have PowerShell and WSL.

1)
Download current version (for example, PowerShell-7.3.0-win-x64.msi)
and install PowerShell

2) setting up WSL2
Open PowerShell in administrator mode and enter
wsl --install
to see a list of available Linux distributions available
for download through the online store
Enter:
wsl --list --online
setting upl a Linux(Ubuntu) distribution environment
wsl --install -d <Distribution Name>.
for example,
wsl --install -d Ubuntu
Setting WSL2 for your Linux distros
wsl --set-default-version 2

3) Installing Ubuntu
Using Microsoft Store, we download Ubuntu.
We do not wish to run installation via MS-Store.
Instead, in Search command:
Ubuntu

This initiates the installation window.
Using the moment, we click on the header with Right-Mouse
to pin the executable (to be able to open Ubuntu terminal)
where we want to.

After installation, we instruct user name and pass:
user: XXXX
pass: XXXX

To create a shortcut to the Ubuntu directory in File Explorer enter
\\wsl$

You will see the folder
Ubuntu (wsl&)

Click on with Right Mouse and create a shortcut to this folder
and place the shortcut where convenient:



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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