Thanks Romain and Scott! We are trying these things, one at a time, until something works.
:-) 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
http://glycam.org
________________________________
From: Romain M. Wolf <romain.wolf.gmail.com>
Sent: Wednesday, April 29, 2020 10:04 PM
To: AMBER Developers Mailing List <amber-developers.ambermd.org>
Subject: Re: [AMBER-Developers] Release candidate 5 for Amber20/AmberTools20
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Regarding CMake.app on Mac:
Open the CMake.app, then choose under Tools "How to Install for Command Line Use", which gives you this:
One may add CMake to the PATH:
PATH="/Applications/CMake.app/Contents/bin":"$PATH"
Or, to install symlinks to '/usr/local/bin', run:
sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
Or, to install symlinks to another directory, run:
sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
I used option 2, which works fine, provided that you have /usr/local/bin in your $PATH, where a symlink is set to:
/Applications/CMake.app/Contents/bin/cmake
Another option might be to install cmake via MacPorts.
...regards...romain
> On 30 Apr 2020, at 07:25, B. Lachele Foley <lfoley.ccrc.uga.edu> 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://tudat.tudelft.nl/installation/setupDevMacOs.html
>
> :-) 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
> http://glycam.org
> ________________________________
> 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 - 20:00:01 PDT
