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!
-Guqin
-----邮件原件-----
发件人: 石谷沁
发送时间: 2021年5月7日 8:49
收件人: AMBER Mailing List <amber.ambermd.org>
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
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<
http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<
http://www.gnu.org/software/autoconf>
<
http://www.gnu.org/software/m4/>
<
http://www.perl.org/>
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:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Amber source found, building AmberTools and Amber
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- 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/amber.sh
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...
https://drive.google.com/drive/folders/1uf5pwdCuKKqOXAvCERXBi_AfwQOVXOUt?usp=sharing
Anyone could help give a hint?...Really need to get things solved for following tasks...
Thank you a lot!!
-Guqin
-----邮件原件-----
发件人: David A Case [mailto:david.case.rutgers.edu]
发送时间: 2021年5月6日 20:14
收件人: AMBER Mailing List <amber.ambermd.org>
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
> 'configure.ac' or m4 files included by 'configure.ac'.
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?
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
***********免责声明*************
本电子邮件中包含的信息仅供指定的或授权的个人或团体使用。本电子邮件及附件中提到的信息可能是保密信息或者法律特许保密的信息。如果你不是指定收件人，对于邮件内容的任何披露、复制、散布或者任何针对邮件内容进行的行为都是违法行为，需要严格禁止。如果您误收该电子邮件，请立即通知本公司并从您的系统中删除全部原始信息。该邮件可能会对您的系统或者数据造成损坏，对此我公司不承担任何责任。除非与公司业务有关，否则本邮件中的观点、结论、或者其它包含在邮件中的信息均为发件人个人行为，并不代表我公司。我公司有权保留对收发邮件的监控权利。
***********Business Email Disclaimer**************
This e-mail and any attachments are meant for the intended recipient only and may contain information belonging to Qilu Pharma that is privileged, confidential, proprietary, and/or otherwise protected or prohibited from disclosure. If you are not the correct recipient or received this e-mail erroneously, please inform the sender immediately and delete this mail from your system. Qilu Pharma state no liability for any damage to your system and data caused by this email. Unless this email is related to the business with the company, otherwise any views or opinions presented in this email are solely from the sender. Qilu Pharma has the right to monitor the sending and receiving of the e-mail.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 07 2021 - 02:00:03 PDT
