Hi,
1. intelmpi 2019.5
Built; parallel np=2 tests running: now at
export TESTsander=/tmp/junk/amber20///bin/sander.MPI; cd pheMTI && ./Run.lambda1
...
Check wiki for further updates.
2. macOS
Well i didn't check your link ... but it smells like what happened to
me: i downloaded the cmake 3.17.2 dmg from cmake.org/download ...
But that got me a cmake app which i found useless.
So i built from source; same download page; follow 3 step instr. at
cmake.org/install; built cmake fine.
Then i edited run_cmake just to insert the full path for cmake since
i installed cmake in my home dir.
Now running run_cmake.
Check wiki for further updates.
scott
On Thu, Apr 30, 2020 at 12:25:27AM +0000, B. Lachele Foley wrote:
> One of the people trying the Mac install had trouble installing cmake. He's using the instructions at the link below. I don't know Mac well at all, but it seems that cmake-gui down in Applications/CMake.app is symlinked to some other folder and it won't run properly to do the install.
>
> Are there other/better instructions to give him?
>
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftudat.tudelft.nl%2Finstallation%2FsetupDevMacOs.html&data=02%7C01%7Csbrozell%40iqb.rutgers.edu%7C9b581be4272044ff6c4b08d7ec9cffe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637238031361870414&sdata=6X%2FJJ6OAYorWX3bqElO8FvsBDD0EOdU8AyxGl6a0c1Q%3D&reserved=0
>
> :-) Lachele
>
> Dr. B. Lachele Foley (she/her/hers)
> Associate Research Scientist
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fglycam.org%2F&data=02%7C01%7Csbrozell%40iqb.rutgers.edu%7C9b581be4272044ff6c4b08d7ec9cffe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637238031361870414&sdata=BealFXq7S9gTRy5Md17vIUJxrAuJvlwzMzbdpnBxdZQ%3D&reserved=0
> ________________________________
> From: Scott Brozell <sbrozell.iqb.rutgers.edu>
> Sent: Wednesday, April 29, 2020 7:55 PM
> To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] Release candidate 5 for Amber20/AmberTools20
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> Hi,
>
> I built and tested RC3 with intel/19.0.5 intelmpi/2019.5.
> And i am at 36% in make install with RC5.
> I searched my dir tree for mpigi and got no hits.
>
>
> Details FWIW:
>
> Currently Loaded Modules:
> 1) xalt/latest 3) gcc-compatibility/8.4.0 5) mkl/2018.0.3 7) cmake/3.16.5
> 2) modules/au2018 4) intel/19.0.5 6) intelmpi/2019.5
>
> (Note to those actually reading this far; mkl/2018.0.3 was unintentional,
> so this may be a rare test of OSC or Amber treatment of out of sync
> mkl and compilers ...)
>
> # Assume this is Linux:
>
> cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
> -DCOMPILER=MANUAL \
> -DCMAKE_C_COMPILER=$OSC_CC \
> -DCMAKE_CXX_COMPILER=$OSC_CXX \
> -DCMAKE_Fortran_COMPILER=$OSC_F90 \
> -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
> -DCOLOR_CMAKE_MESSAGES=FALSE \
> 2>&1 | tee cmake.log
>
> OSC_CC=icc
> OSC_COMPILER=intel
> OSC_COMPILER_MAJOR=19
> OSC_COMPILER_MINOR=0
> OSC_CXX=icpc
> OSC_F77=ifort
> OSC_F90=ifort
>
> scott
>
> On Wed, Apr 29, 2020 at 04:11:04PM -0400, Daniel Roe wrote:
> > For the parallel build, I can't get RC5 to get past the initial
> > run_cmake phase with Intel 17.0.4 + Intel MPI + cmake 3.13.2:
> >
> > ```
> > -- Could NOT find MPI_C (missing: MPI_mpigi_LIBRARY MPI_C_WORKS)
> > -- Could NOT find MPI_CXX (missing: MPI_mpigi_LIBRARY MPI_CXX_WORKS)
> > -- Could NOT find MPI_Fortran (missing: MPI_mpigi_LIBRARY MPI_Fortran_WORKS)
> > -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND)
> > CMake Error at cmake/MPIConfig.cmake:12 (message):
> > You requested MPI, but the MPI C library was not found. Please install one
> > and try again, or set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES to point to
> > your MPI.
> > Call Stack (most recent call first):
> > CMakeLists.txt:118 (include)
> > ```
> >
> > Run after setting -DCOMILER to INTEL, and -DMPI and -DCUDA to TRUE.
> > CMakeOutput.log is quite monolithic and it's not immediately clear to
> > me what's going wrong (I can send it to interested parties if needed).
> > The serial cmake (-DMPI=FALSE -DCUDA=FALSE) + install works. Note that
> > the parallel cmake fails even after the serial cmake + install
> > succeeds. Legacy configure works normally.
> >
>
> On Wed, Apr 29, 2020 at 06:54:02PM -0400, Brent Krueger wrote:
> > Gerald -- CentOS 8 with MPICH does seem to be working for me. Build was
> > find and tests are ongoing -- but most/all seem to be passing so far.
> >
> > However, I can NOT build CUDA (either 10.1 or 10.2) with CentOS 8
> > successfully anymore. Both 10.1 and 10.2 worked fine with CentOS 8 for me
> > with RC4 and RC3.
> >
> > Brent
> >
> >
> > On Wed, Apr 29, 2020 at 4:57 PM David A Case <david.case.rutgers.edu> wrote:
> >
> > > On Wed, Apr 29, 2020, Dan Roe wrote:
> > >
> > > >For the parallel build, I can't get RC5 to get past the initial
> > > >run_cmake phase with Intel 17.0.4 + Intel MPI + cmake 3.13.2:
> > >
> > > Is this a regression? That is, did earlier release candidates work? If
> > > so, be sure to let Jamie know (see below), as this can probably be fixed.
> > >
> > > I don't have Intel MPI, (it's quite expensive) so can't test what you
> > > are trying. I've built my own MPI using mpich and the intel compilers
> > > (i.e. configure_mpich intel) -- will try that out soon.
> > >
> > > I can confirm that serial intel works pretty well (see wiki test results
> > > site). I'm testing version 19.0.5.
> > >
> > >
> > > >
> > > >```
> > > >-- Could NOT find MPI_C (missing: MPI_mpigi_LIBRARY MPI_C_WORKS)
> > > >-- Could NOT find MPI_CXX (missing: MPI_mpigi_LIBRARY MPI_CXX_WORKS)
> > > >-- Could NOT find MPI_Fortran (missing: MPI_mpigi_LIBRARY
> > > MPI_Fortran_WORKS)
> > > >-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND
> > > MPI_Fortran_FOUND)
> > > >CMake Error at cmake/MPIConfig.cmake:12 (message):
> > > > You requested MPI, but the MPI C library was not found. Please install
> > > one
> > > > and try again, or set MPI_C_INCLUDE_PATH and MPI_C_LIBRARIES to point to
> > > > your MPI.
> > >
> > > Be sure that you get problem reports to Jamie
> > > <jsmith.crackofdawn.onmicrosoft.com>, since I doubt that he follows the
> > > amber-developers mailing list.
> > >
> > > I can't find any Google hits on MPI_mpigi_LIBRARY. You might try
> > > setting your CMAKE_PREFIX_PATH variable to the location of the intel MPI
> > > library.
> > >
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Received on Wed Apr 29 2020 - 18:30:03 PDT
