Thank you very much. When I run the nproc command to know how many processors I have available it print 8
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: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, February 18, 2020 2:03 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.
Hi,
On Mon, Feb 17, 2020 at 6:28 PM Nicolas Feldman <nfeldman01.qub.ac.uk> wrote:
>
> 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.
This means that you requested 8 MPI processes, but the hardware you are trying to run on does not have 8 available processes. As a rough estimate of what your system will currently support, run `nproc`. If you're running on a batch queuing system (like SLURM), the number of available processes will depend on how the system is configured.
OpenMPI will let you "oversubscribe", but performance will be poor.
See
https://www.open-mpi.org/faq/?category=running#oversubscribing for more info.
-Dan
> 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.dif
> f
> 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>
> 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-window
> > > s1
> > > 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>
> > > 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
> > > > _______________________________________________
> > > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Tue Feb 18 2020 - 07:00:02 PST
