Nice! Let us know how it went!
Regards!
Gera!
El lun., 17 de feb. de 2020 19:56, Gustaf Olsson <gustaf.olsson.lnu.se>
escribió:
> Good to hear, feel free to reach out at any point if you have any more
> problems.
>
>
> Keeping the instructions accurate and up to date is challenging and
> sometimes I do need a push.
>
>
> Best regards
>
> // Gustaf
>
> ________________________________
> Från: Nicolas Feldman <nfeldman01.qub.ac.uk>
> Skickat: den 17 februari 2020 23:53:36
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] installing
>
> I had forget a previous command, now im installing and should be fine.
> Indeed im in a WSL
>
> Nicolas Feldman
> PhD Student
> The Wellcome-Wolfson Institute for Experimental Medicine
> Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
>
> -----Original Message-----
> From: Gustaf Olsson <gustaf.olsson.lnu.se>
> Sent: Monday, February 17, 2020 10:47 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] installing
>
> This message is from an external sender. Please take care when responding,
> clicking links or opening attachments.
>
> I am not sure what you are trying to accomplish?
>
>
> Am I correct in assumeing you are trying to compile Amber or AmberTools in
> Windows Subsystem for Linux? Have you chosen Ubuntu or another *nix version?
>
>
> Whatever is available on the website was tested when it was published.
> There are no guarantees that it still is accurate. As discussed with
> another user last week (?) I did recompile the latest version of AmberTools
> in WSL Ubuntu, the serial version without error. I also recompiled serial
> and both MPI and OpenMPI on Ubuntu as well as serial and MPI versions on
> Mac last week.
>
>
> This: FFTW configure failed! To me seems like you either had a problem
> installing the prerequisites or had problems with the miniconda
> installation of prerequisites. This --enable-mpi is not an option addressed
> on the website at any point.
>
>
> You do not have to install the parallel version of you have a successful
> serial installation present. However, I doubt that you would if you have
> this configuration error FFTW configure failed! This should break the
> serial configuration as well.
>
>
> So, you are a Windows 10 user and you have installed some Linux version
> from the "windows store". Is it Ubuntu? Which version, what have you done
> so far in terms of commands? Feel free to email me directly if you prefer,
> I am on a short leave until Thursday though I check my email sporadically.
>
>
> I am planning to update the available instructions as well as adding
> direct Ubuntu instructions as soon as possible though getting a clean VM
> for each OS setup and running usually takes longer then I anticipate.
>
>
> Best regards
>
> // Gustaf
>
>
> ________________________________
> Från: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> Skickat: den 17 februari 2020 22:32:30
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] installing
>
> Hi again!
> I copy a thread that is relates to you issue. Give it a try:
>
> On Mon, May 29, 2017, Lucas wrote:
> *>*
> *> Last year a user posted the message in the end of the mail about the*
> *> common error " could not find mpi library for --enable-mpi"*
> *>*
> *> I'm running into the same problem, and from the response given then it*
> *> means either the user doesn't have an mpi library installed or it is* *>
> not in LD_LIBRARY_PATH*
>
> This is a difficult problem, and (notwithstanding the earlier reply)
> probably has nothing to do with LD_LIBRARY_PATH.
>
> *>*
> *> So I installed mpich,*
>
> The problem is that we don't know what to you did to "install mpich", and
> debugging the fftw parallel installtion procedure is a task beyond my
> comfort zone.
>
> If you are on Linux, make sure that you install both the mpich *and* the
> mpich-dev (or mpich-devel) libraries.
>
> But my best suggestion is this, which is what we almost always suggest for
> mpi problems:
>
> cd $AMBERHOME/AmberTools/src
> ./configure_mpich gnu
>
> (You may have to download the code, as explained in the output to the
> above command.) This sets up all the MPI directories *within* the AMBERHOME
> directory tree, and ensures that you will have the proper functions like
> mpicc and mpif90 available (assuming that $AMBERHOME/bin comes before any
> other mpi stuff in your $PATH.
>
> ..give this a try....dac
>
> El lun., 17 de feb. de 2020 18:11, Nicolas Feldman <nfeldman01.qub.ac.uk>
> escribió:
>
> > What I mean is : I do not know the purpose of mpi. Im just following
> > the introction to install amber.
> > https://www.ovetande.se/software/amber/install/ambertools19-windows10-
> > wsl/
> >
> > Nicolas Feldman
> > PhD Student
> > The Wellcome-Wolfson Institute for Experimental Medicine Queen's
> > University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> >
> > -----Original Message-----
> > From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> > Sent: Monday, February 17, 2020 9:07 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] installing
> >
> > This message is from an external sender. Please take care when
> > responding, clicking links or opening attachments.
> >
> > Are you trying to install serial amber or parallel (mpi)?
> > Regards!
> > Gera
> >
> > El lun., 17 de feb. de 2020 17:56, Nicolas Feldman
> > <nfeldman01.qub.ac.uk>
> > escribió:
> >
> > > It seem that I do not have the mpi library, because: configure: error:
> > > could not find mpi library for --enable-mpi
> > >
> > > I did the following that you recommend and receive this output:
> > >
> > >
> > > checking for a BSD-compatible install... /usr/bin/install -c
> > >
> > > checking whether build environment is sane... yes
> > >
> > > checking for a thread-safe mkdir -p... /bin/mkdir -p
> > >
> > > checking for gawk... gawk
> > >
> > > checking whether make sets $(MAKE)... yes
> > >
> > > checking whether to enable maintainer-specific portions of Makefiles...
> > > no
> > > checking build system type... x86_64-unknown-linux-gnu
> > >
> > > checking host system type... x86_64-unknown-linux-gnu
> > >
> > > checking for gcc... gcc
> > >
> > > checking whether the C compiler works... yes
> > >
> > > checking for C compiler default output file name... a.out
> > >
> > > checking for suffix of executables...
> > >
> > > checking whether we are cross compiling... no
> > >
> > > checking for suffix of object files... o
> > >
> > > checking whether we are using the GNU C compiler... yes
> > >
> > > checking whether gcc accepts -g... yes
> > >
> > > checking for gcc option to accept ISO C89... none needed
> > >
> > > checking for style of include used by make... GNU
> > >
> > > checking dependency style of gcc... gcc3
> > >
> > > checking whether gcc and cc understand -c and -o together... yes
> > >
> > > checking for C compiler vendor... gnu
> > >
> > > checking for gcc option to accept ISO C99... none needed
> > >
> > > checking for gcc option to accept ISO Standard C... (cached) none
> > > needed
> > >
> > > checking whether ln -s works... yes
> > >
> > > checking whether make sets $(MAKE)... (cached) yes
> > >
> > > checking for a sed that does not truncate output... /bin/sed
> > >
> > > checking for grep that handles long lines and -e... /bin/grep
> > >
> > > checking for egrep... /bin/grep -E
> > >
> > > checking for fgrep... /bin/grep -F
> > >
> > > checking for ld used by gcc... /usr/bin/ld
> > >
> > > checking if the linker (/usr/bin/ld) is GNU ld... yes
> > >
> > > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
> > > -B
> > >
> > > checking the name lister (/usr/bin/nm -B) interface... BSD nm
> > >
> > > checking the maximum length of command line arguments... 1572864
> > >
> > > checking whether the shell understands some XSI constructs... yes
> > >
> > > checking whether the shell understands "+="... yes
> > >
> > > checking for /usr/bin/ld option to reload object files... -r
> > >
> > > checking for objdump... objdump
> > >
> > > checking how to recognize dependent libraries... pass_all
> > >
> > > checking for ar... ar
> > >
> > > checking for strip... strip
> > >
> > > checking for ranlib... ranlib
> > >
> > > checking command to parse /usr/bin/nm -B output from gcc object...
> > > ok
> > >
> > > checking how to run the C preprocessor... gcc -E
> > >
> > > checking for ANSI C header files... yes
> > >
> > > checking for sys/types.h... yes
> > >
> > > checking for sys/stat.h... yes
> > >
> > > checking for stdlib.h... yes
> > >
> > > checking for string.h... yes
> > >
> > > checking for memory.h... yes
> > >
> > > checking for strings.h... yes
> > >
> > > checking for inttypes.h... yes
> > >
> > > checking for stdint.h... yes
> > >
> > > checking for unistd.h... yes
> > >
> > > checking for dlfcn.h... yes
> > >
> > > checking for objdir... .libs
> > >
> > > checking if gcc supports -fno-rtti -fno-exceptions... no
> > >
> > > checking for gcc option to produce PIC... -fPIC -DPIC
> > >
> > > checking if gcc PIC flag -fPIC -DPIC works... yes
> > >
> > > checking if gcc static flag -static works... yes
> > >
> > > checking if gcc supports -c -o file.o... yes
> > >
> > > checking if gcc supports -c -o file.o... (cached) yes
> > >
> > > checking whether the gcc linker (/usr/bin/ld -m elf_x86_64)
> > > supports shared libraries... yes checking
> dynamic
> > > linker characteristics... GNU/Linux ld.so
> > >
> > > checking how to hardcode library paths into programs... immediate
> > >
> > > checking whether stripping libraries is possible... yes
> > >
> > > checking if libtool supports shared libraries... yes
> > >
> > > checking whether to build shared libraries... no
> > >
> > > checking whether to build static libraries... yes
> > >
> > > checking for ocamlbuild... no
> > >
> > > checking for mpicc... no
> > >
> > > checking for hcc... no
> > >
> > > checking for mpcc... no
> > >
> > > checking for mpcc_r... no
> > >
> > > checking for mpxlc... no
> > >
> > > checking for cmpicc... no
> > >
> > > checking for MPI_Init... no
> > >
> > > checking for MPI_Init in -lmpi... no
> > >
> > > checking for MPI_Init in -lmpich... no
> > >
> > > configure: error: could not find mpi library for --enable-mpi
> > >
> > > -----Original Message-----
> > > From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> > > Sent: Monday, February 17, 2020 8:49 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] installing
> > >
> > > This message is from an external sender. Please take care when
> > > responding, clicking links or opening attachments.
> > >
> > > Edit
> > > Do the following:
> > >
> > > cat /home/nico/amber18/AmberTools/src/fftw3_config.log
> > >
> > >
> > > El lun., 17 de feb. de 2020 17:48, Gerardo Zerbetto De Palma <
> > > g.zerbetto.gmail.com> escribió:
> > >
> > > > Hi again!
> > > > Just to make it clear: Are those the contents of fftw3_config.log
> file?
> > > > In case not, just do the following:
> > > >
> > > > cat /home/nico/amber18/AmberTools/src
> > > >
> > > > and paste contents here.
> > > > Regards
> > > > Gera!
> > > >
> > > > El lun., 17 de feb. de 2020 17:41, Nicolas Feldman
> > > > <nfeldman01.qub.ac.uk>
> > > > escribió:
> > > >
> > > >> Everything seems okey until this last few lines where a error is
> > > >> display
> > > >>
> > > >> Checking for zlib: OK
> > > >>
> > > >>
> > > >> Checking for libbz2: OK
> > > >>
> > > >>
> > > >> Configuring fftw-3.3 (may be time-consuming)...
> > > >>
> > > >>
> > > >> Error: FFTW configure returned 1
> > > >>
> > > >> FFTW configure failed! Check the fftw3_config.log file
> > > >>
> > > >> in the /home/nico/amber18/AmberTools/src directory.
> > > >>
> > > >> Configure failed due to the errors above!
> > > >>
> > > >> Nicolas Feldman
> > > >> PhD Student
> > > >> The Wellcome-Wolfson Institute for Experimental Medicine Queen's
> > > >> University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> > > >>
> > > >> -----Original Message-----
> > > >> From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> > > >> Sent: Monday, February 17, 2020 8:39 PM
> > > >> To: AMBER Mailing List <amber.ambermd.org>
> > > >> Subject: Re: [AMBER] installing
> > > >>
> > > >> This message is from an external sender. Please take care when
> > > >> responding, clicking links or opening attachments.
> > > >>
> > > >> Share that error log with us!
> > > >> Regards
> > > >> Gera!
> > > >>
> > > >> El lun., 17 de feb. de 2020 17:36, Nicolas Feldman
> > > >> <nfeldman01.qub.ac.uk>
> > > >> escribió:
> > > >>
> > > >> > I'm getting this error when installing:
> > > >> > Error: FFTW configure returned 1 FFTW configure failed! Check
> > > >> > the fftw3_config.log file in the
> > > >> > /home/[user]/amber18/AmberTools/src directory.
> > > >> > Configure failed due to the errors above!
> > > >> >
> > > >> > Nicolas Feldman
> > > >> > PhD Student
> > > >> > The Wellcome-Wolfson Institute for Experimental Medicine
> > > >> > Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9
> > > >> > 7BL
> > > >> >
> > > >> > _______________________________________________
> > > >> > AMBER mailing list
> > > >> > AMBER.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >> >
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> >
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Received on Mon Feb 17 2020 - 15:30:02 PST
