Re: [AMBER] installing

From: Nicolas Feldman <nfeldman01.qub.ac.uk>
Date: Tue, 18 Feb 2020 00:14:09 +0000

Testing

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________________________________
From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
Sent: Tuesday, February 18, 2020 12:10:45 AM
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.

So does this error popped when compilimg amber or when testing?

El lun., 17 de feb. de 2020 20:28, Nicolas Feldman <nfeldman01.qub.ac.uk>
escribiˇ:

> So it seem that I reach another error after:
>
> export DO_PARALLEL="mpirun -np $(nproc)"
> make test
>
>
> There are not enough slots available in the system to satisfy the 8
>
> slots that were requested by the application:
>
>
> /home/nico_amber/amber18/bin/sander.MPI
>
>
> Either request fewer slots for your application, or make more
> slots
> available for use.
>
>
>
> A "slot" is the Open MPI term for an allocatable unit where we can
>
> launch a process. The number of slots available are defined by the
>
> environment in which Open MPI processes are run:
>
>
> 1. Hostfile, via "slots=N" clauses (N defaults to number of
>
> processor cores if not provided)
>
> 2. The --host command line parameter, via a ":N" suffix on the
>
> hostname (N defaults to 1 if not provided)
>
> 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
>
> 4. If none of a hostfile, the --host command line parameter, or an
>
> RM is present, Open MPI defaults to the number of processor cores
>
>
> In all the above cases, if you want Open MPI to default to the number
>
> of hardware threads instead of the number of processor cores, use the
>
> --use-hwthread-cpus option.
>
>
> Alternatively, you can use the --oversubscribe option to ignore the
>
> number of available slots when deciding the number of processes to
>
> launch.
>
> --------------------------------------------------------------------------
>
> ./min.csh: Program error
>
> Makefile:296: recipe for target 'test.parallel.sander.SEBOMD' failed
>
> make[2]: [test.parallel.sander.SEBOMD] Error 1 (ignored)
>
> make[2]: Target 'test.parallel.at' not remade because of errors.
>
> make[2]: Leaving directory '/home/nico_amber/amber18/test'
>
> make[2]: Entering directory '/home/nico_amber/amber18/AmberTools/test'
>
>
> Finished test suite for AmberTools at Mon Feb 17 23:18:23 GMT
> 2020.
>
> make[2]: Leaving directory
> '/home/nico_amber/amber18/AmberTools/test'
>
> 5 file comparisons passed
>
> 642 file comparisons failed (0 ignored)
>
> 686 tests experienced errors
>
> Test log file saved as
> /home/nico_amber/amber18/logs/test_at_parallel/2020-02-17_23-15-10.log
>
> Test diffs file saved as
> /home/nico_amber/amber18/logs/test_at_parallel/2020-02-17_23-15-10.diff
>
> Makefile:14: recipe for target 'test.parallel' failed
>
> make[1]: *** [test.parallel] Error 1
>
> make[1]: Leaving directory '/home/nico_amber/amber18/AmberTools/test'
>
> Makefile:91: recipe for target 'test.parallel' failed
>
> make: [test.parallel] Error 2 (ignored)
>
> ==============================================================
>
> /home/nico_amber/amber18/src/Makefile not found.
>
> This is expected if you have not installed Amber18.
>
>
> 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 11:21 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.
>
> Nice! Let us know how it went!
> Regards!
> Gera!
>
> El lun., 17 de feb. de 2020 19:56, Gustaf Olsson <gustaf.olsson.lnu.se>
> escribiˇ:
>
> > 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
> >
> > ________________________________
> > Frňn: Nicolas Feldman <nfeldman01.qub.ac.uk>
> > Skickat: den 17 februari 2020 23:53:36
> > Till: AMBER Mailing List
> > ─mne: 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
> >
> >
> > ________________________________
> > Frňn: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> > Skickat: den 17 februari 2020 22:32:30
> > Till: AMBER Mailing List
> > ─mne: 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>
> > escribiˇ:
> >
> > > 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-windows1
> > > 0-
> > > 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>
> > > escribiˇ:
> > >
> > > > 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> escribiˇ:
> > > >
> > > > > 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>
> > > > > escribiˇ:
> > > > >
> > > > >> 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>
> > > > >> escribiˇ:
> > > > >>
> > > > >> > 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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> > > > 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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> >
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> >
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Received on Mon Feb 17 2020 - 16:30:03 PST
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