Hi again!
Can you run *lscpu* and show us the output?
You may also try to do:
*export DO_PARALLEL="mpirun -np 2" make test*
Just to see if it works requesting 2 processes, instead of 8.
Regards
Gera
El mar., 18 feb. 2020 a las 11:34, Nicolas Feldman (<nfeldman01.qub.ac.uk>)
escribió:
> 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
> > >
> > > _______________________________________________
> > > 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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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 18 2020 - 07:00:02 PST
