[CP2K-user] [CP2K:19617] graph compilation

Victor Volkov volkovskr at gmail.com
Fri Dec 1 11:41:28 UTC 2023
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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>
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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Thursday, 30 November 2023 at 13:34
> *To: *cp2k at googlegroups.com <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>
> 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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Thursday, 30 November 2023 at 09:14
> *To: *cp2k at googlegroups.com <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>
> 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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Sunday, 26 November 2023 at 14:21
> *To: *cp2k at googlegroups.com <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>
> 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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Tuesday, 21 November 2023 at 09:40
> *To: *cp2k at googlegroups.com <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>
> 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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Thursday, 6 July 2023 at 19:18
> *To: *cp2k at googlegroups.com <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>
> wrote:
>
> Dear Victor
>
>
>
> Try just
>
>
>
> make ARCH=Linux-x86-64-gfortran VERSION=sopt fes
>
>
>
> HTH
>
>
>
> Matthias
>
>
>
> *From: *cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Thursday, 6 July 2023 at 18:46
> *To: *cp2k at googlegroups.com <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>
> 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 <cp2k at googlegroups.com> on behalf of Victor
> Volkov <volkovskr at gmail.com>
> *Date: *Tuesday, 27 June 2023 at 21:14
> *To: *cp2k <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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