Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich

From: 石谷沁 <>
Date: Fri, 7 May 2021 08:53:34 +0000

Dear David,

Somehow I don't know why configuration/installation of mpich.3.3.2 under amber20_src/AmberTools/src failed/incompleted...

I install mpich.3.3.2 separately under /opt and export the PATH.
By doing so, run_cmake could find the mpicc and mpicrun successfully.

I installed the parallel module successfully now.

Thank you a lot for your input!

发件人: 石谷沁
发送时间: 2021年5月7日 8:49
收件人: AMBER Mailing List <>
主题: 答复: [ambermd.org代发]Re: [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich

I re-produced the error here:

For the first try, below is the tail of mpi configure reports:
checking for GNU libc compatible malloc... yes checking for memset... yes checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating include/Makefile
config.status: creating src/Makefile
config.status: creating dtpoolsconf.h
config.status: executing depfiles commands
config.status: executing libtool commands Configuration completed.
    MPICH configure succeeded.
    (You may need to add /opt/amber20/lib to your LD_LIBRARY_PATH) ( cd ./src/binding/fortran/mpif_h && ./buildiface ) ( cd ./src/binding/fortran/use_mpi && ./buildiface ) CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /opt/amber20_src/AmberTools/src/mpich-3.3.2/confdb/missing aclocal-1.15 -I confdb -I src/hwloc/config
/opt/amber20_src/AmberTools/src/mpich-3.3.2/confdb/missing: line 81: aclocal-1.15: command not found
WARNING: 'aclocal-1.15' is missing on your system.
         You should only need it if you modified 'acinclude.m4' or
         '' or m4 files included by ''.
         The 'aclocal' program is part of the GNU Automake package:
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
make: *** [Makefile:10608: aclocal.m4] Error 127 =======================================================================================================================================

If ignoring the WARNING here, I go back to /opt/amber20_src/build, edit run_cmake, turning -DMPI flag to TRUE.
Then immediately get following error:
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.17.5
-- For how to use this build system, please read this wiki:
-- For a list of important CMake variables, check here:
-- **************************************************************************
-- Amber source found, building AmberTools and Amber
-- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIB_NAMES MPI_Fortran_F77_HEADER_DIR MPI_Fortran_MODULE_DIR 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!
See also "/opt/amber20_src/build/CMakeFiles/CMakeOutput.log".
See also "/opt/amber20_src/build/CMakeFiles/CMakeError.log".

If the cmake build report looks OK, you should now do the following:

    make install
    source /opt/amber20/

Consider adding the last line to your login startup script, e.g. ~/.bashrc =======================================================================================================================================

I'm confused here if the MPICH is configure correctly, but the PATH was not set, OR the MPICH is not configured correctly....?
If I configured the mpich under /opt/amber20_src/AmberTools/src, then the mpich path should be $AMBERHOME?

I uploaded the CMakeOuput.log and CMakeError.log here...

Anyone could help give a hint?...Really need to get things solved for following tasks...

Thank you a lot!!

发件人: David A Case []
发送时间: 2021年5月6日 20:14
收件人: AMBER Mailing List <>
主题: [ambermd.org代发]Re: [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich

On Thu, May 06, 2021, 石谷沁 wrote:

>Error reported that aclocal-1.15 is missing on your system…
>WARNING: 'aclocal-1.15' is missing on your system.
> You should only need it if you modified 'acinclude.m4' or
> '' or m4 files included by ''.

The message indicates that this is just a warning, not an error. You should not need aclocal to install mpich. What happens if you just ignore the warning?


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Received on Fri May 07 2021 - 02:00:03 PDT
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