Dear Amber developers/users,
I am trying to install AmberTools20 in parallel on Cluster that works with
CentOS 6 and OpenMPI. The first time I ran the command "./run cmake" to
install the serial version I got the following output:
If you can't see the following build report, then you need to turn off
COLOR_CMAKE_MESSAGES
- ************************************************
**************************
- Build Report
- Compiler Flags:
- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O0
- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune = native
-
- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O0
- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O3 -mtune = native
-
- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0
- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3
-mtune = native
-
- 3rd Party Libraries
- --- building bundled: ------------------------------------------
-----------
- arpack - for fundamental linear algebra calculations
- ucpp - used as a preprocessor for the NAB compiler
- netcdf - for creating trajectory data files
- netcdf-fortran - for creating trajectory data files from Fortran
- fftw - used to do Fourier transforms very quickly
- xblas - used for high-precision linear algebra calculations
- boost - C ++ support library
- perlmol - chemistry library used by FEW
- --- using installed: ------------------------------------------
------------
- blas - for fundamental linear algebra calculations
- lapack - for fundamental linear algebra calculations
- readline - used for the console functionality of cpptraj
- zlib - for various compression and decompression tasks
- libbz2 - for bzip2 compression in cpptraj
- libm - for fundamental math routines if they are not contained in the C
library
- --- disabled: ------------------------------------------- -----
- c9x-complex - used as a support library on systems that do not have C99
complex.h support
- lio - used by Sander to run certain QM routines on the GPU
- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
- pupil - used by Sander as an alternate user interface
- plumed - used as an alternate MD backend for Sander
- mkl - alternate implementation of lapack and blas that is tuned for speed
- Features:
- MPI: OFF
- OpenMP: OFF
- CUDA: OFF
- Build Shared Libraries: ON
- Build GUI Interfaces: ON
- Build Python Programs: ON
- -Python Interpreter: Internal Miniconda (version 3.8)
- Build Perl Programs: ON
- Build configuration: RELEASE
- Target Processor: x86_64
- Build Documentation: OFF
- Sander Variants: normal LES API LES-API
- Install location: /home/apps/Chem/AmberTools20/amber20/
- Installation of Tests: ON
- Compilers:
- C: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin / gcc)
- CXX: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin / g ++)
- Fortran: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin /
gfortran)
The installation was successful and then I started the "make test.serial"
to verify the installation. Everything seemed to be in order except some
tests with the same warning:
"/ opt / rh / devtoolset-8 / root / usr / libexec / gcc /
x86_64-redhat-linux / 8 / ld: warning: libgfortran.so.3, needed by
/usr/lib64/libopenblas.so, may conflict with libgfortran.so.5
/ opt / rh / devtoolset-8 / root / usr / libexec / gcc /
x86_64-redhat-linux / 8 / ld: warning: libgfortran.so.3, needed by
/usr/lib64/libopenblas.so, may conflict with libgfortran .so.5 "
Then I tried to install the parallel version of AmberTools20, I ran the
command "./run_cmake" again (indicating before the PATH of mpicc and
mpif90) and the output was the following:
If you can't see the following build report, then you need to turn off
COLOR_CMAKE_MESSAGES
- ************************************************
**************************
- Build Report
- Compiler Flags:
- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O0
- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune = native
-
- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O0
- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-local-typedefs -Wno-unused-variable
-Wno-unused-but-set-variable -O3 -mtune = native
-
- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0
- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function
-ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3
-mtune = native
-
- 3rd Party Libraries
- --- building bundled: ------------------------------------------
-----------
- arpack - for fundamental linear algebra calculations
- ucpp - used as a preprocessor for the NAB compiler
- netcdf - for creating trajectory data files
- netcdf-fortran - for creating trajectory data files from Fortran
- fftw - used to do Fourier transforms very quickly
- xblas - used for high-precision linear algebra calculations
- boost - C ++ support library
- mpi4py - MPI support library for MMPBSA.py
- pnetcdf - used by cpptraj for parallel trajectory output
- --- using installed: ------------------------------------------
------------
- blas - for fundamental linear algebra calculations
- lapack - for fundamental linear algebra calculations
- readline - used for the console functionality of cpptraj
- zlib - for various compression and decompression tasks
- libbz2 - for bzip2 compression in cpptraj
- libm - for fundamental math routines if they are not contained in the C
library
- perlmol - chemistry library used by FEW
- --- disabled: ------------------------------------------- -----
- c9x-complex - used as a support library on systems that do not have C99
complex.h support
- lio - used by Sander to run certain QM routines on the GPU
- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
- pupil - used by Sander as an alternate user interface
- plumed - used as an alternate MD backend for Sander
- mkl - alternate implementation of lapack and blas that is tuned for speed
- Features:
- MPI: ON
- OpenMP: OFF
- CUDA: OFF
- Build Shared Libraries: ON
- Build GUI Interfaces: ON
- Build Python Programs: ON
- -Python Interpreter: Internal Miniconda (version 3.8)
- Build Perl Programs: ON
- Build configuration: RELEASE
- Target Processor: x86_64
- Build Documentation: OFF
- Sander Variants: normal LES API LES-API MPI LES-MPI
- Install location: / home / apps / Chem / AmberTools20 / amber20 /
- Installation of Tests: ON
- Compilers:
- C: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin / gcc)
- CXX: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin / g ++)
- Fortran: GNU 8.3.1 (/ opt / rh / devtoolset-8 / root / usr / bin /
gfortran)
Amber has correctly recognized the MPI as it is now ON, and I ran the "make
install" command again to install the parallel version this time. The
parallel version seemed to be installed correctly (except for some
warnings) but one I ran the command "make test.parallel" to check if
everything was correct, almost all the tests had given me an error (I
attach the logs of the version tests in parallel). All the errors seem to
be linked to these warnings:
" / opt / rh / devtoolset-8 / root / usr / libexec / gcc /
x86_64-redhat-linux / 8 / ld: warning: libgfortran.so.3, needed by
/usr/lib64/libopenblas.so, may conflict with libgfortran.so.5
/ opt / rh / devtoolset-8 / root / usr / libexec / gcc /
x86_64-redhat-linux / 8 / ld: warning: libgfortran.so.3, needed by
/usr/lib64/libopenblas.so, may conflict with libgfortran .so.5 "
"/opt/intel/composer_xe_2013.0.079/mpirt/bin/intel64/mpirun: line 96:
/opt/intel/composer_xe_2013.0.079/mpirt/bin/intel64/mpivars.sh: No such
file or directory
[mpiexec.celestina] HYDU_create_process (./utils/launch/launch.c:102):
execvp error on file
/opt/intel/composer_xe_2013.0.079/mpirt/bin/intel64/pmi_proxy (No such file
or directory)"
But I'm not very sure and I don't know how I could solve it. Could someone
take a look at the logs and help me fix this problem?
Thank you very much for your help.
Alain
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Received on Thu Feb 25 2021 - 03:00:03 PST
