Hi all,
According to Jamie there was a change between RC4 and RC5 how cmake finds
shared and static libraries. This broke my iAPBS build in similar way the
MPI build is broken. Jamie provided a fix for my builds but I guess this
needs to addressed in more general way?
Best,
Robert
On Wed, Apr 29, 2020 at 09:46:56PM -0400, Scott Brozell wrote:
>Hi,
>
>Sweet vindication for Dan:
>
>Currently Loaded Modules:
> 1) xalt/latest 3) cxx17/7.3.0 5) intelmpi/2017.4
> 2) modules/au2018 4) intel/17.0.7 6) cmake/3.11.4
>
>-- Testing if stdlib.h can be included... yes
>-- 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)
>
>
>-- Configuring incomplete, errors occurred!
>
>din din time, might investigate tonight...
>
>scott
>
>On Wed, Apr 29, 2020 at 09:15:58PM -0400, Scott Brozell wrote:
>> 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://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Ftudat.tudelft.nl*2Finstallation*2FsetupDevMacOs.html&data=02*7C01*7Csbrozell*40iqb.rutgers.edu*7C39c56f69b5e64c720a7208d7eca40e91*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C637238061673791727&sdata=LQVrlzLDLL5*2BV3H5PpDB6PjotYHNYg*2BY426MXMQleoY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!XRkORm8yUm94Wpp0l_JBD20wNycULuD_yQK8BNCHv2rGRvHZZMNXG-ug8BXv$
>> >
>> > :-) 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://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=http*3A*2F*2Fglycam.org*2F&data=02*7C01*7Csbrozell*40iqb.rutgers.edu*7C39c56f69b5e64c720a7208d7eca40e91*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C637238061673791727&sdata=l*2B*2Fg0*2FZUXjGa7IhpgGLjBBXQjTfOnQbdCV6fs6LskxE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!XRkORm8yUm94Wpp0l_JBD20wNycULuD_yQK8BNCHv2rGRvHZZMNXG38utAUQ$
>> > ________________________________
>> > 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.
>> > > >
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> https://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=http*3A*2F*2Flists.ambermd.org*2Fmailman*2Flistinfo*2Famber-developers&data=02*7C01*7Csbrozell*40iqb.rutgers.edu*7C39c56f69b5e64c720a7208d7eca40e91*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C637238061673791727&sdata=FFRpW8IIQY31jjMQZv3WNXnZEw8GQRNDCmBwijVDcpE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUl!!Mih3wA!XRkORm8yUm94Wpp0l_JBD20wNycULuD_yQK8BNCHv2rGRvHZZMNXGxvnqoh8$
>
>_______________________________________________
>AMBER-Developers mailing list
>AMBER-Developers.ambermd.org
>https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber-developers__;!!Mih3wA!XRkORm8yUm94Wpp0l_JBD20wNycULuD_yQK8BNCHv2rGRvHZZMNXG_8deuSL$
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Apr 30 2020 - 07:00:02 PDT
