[CP2K-user] [CP2K:19618] graph compilation

Victor Volkov volkovskr at gmail.com
Fri Dec 1 12:03:05 UTC 2023
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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>
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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