[CP2K-user] [CP2K:19540] graph compilation

Victor Volkov volkovskr at gmail.com
Tue Nov 21 10:15:46 UTC 2023
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Dear Matthias:

During Summer and Autumn, I did invest into WSL-Ubuntu.
The original drive was to learn tleap and antechamber to prepare topologies
for ligands.
In result, I did manage the key steps,
which are not explained (but granted) in the CP2K QMMM tutorial for
Chorismate Mutase.

Since it took, half of year (in 2021) to learn how to install CP2K under
cygwin,
I got somewhat reluctant to spent another 6 month battling to manage the
same under WSL.

In mean time, there are several articles to finish
and several long-term CP2K jobs under cygwin.

Being isolated in the Russian country side without any support,
but what I was growing and brewing in the summer, I may not have that much
time in my age and under my conditions.
Since the state rep has my anti-war statement in written - it is up to them
to place me in a penal colony for 7 years, any time.

Therefore, by now, I failed to force self to reserve time with the black
screen on WSL CP2K.

In principle, you are right - I should do.

On the other hand,
since I use Mathematica for 20 years, if having equations,
trying to program (rather than having passive hopes into "problematic
handouts")
may seem to be a good math-programming time investment.
This is why I posted the "sort of" simple question.

I hope you would forgive.

Sincerely,
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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