GNU GCC

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Compiling GCC 12.1.0 on Rocky Linux 8.5

Step 1: Download the following prerequisites applications libraries from https://gcc.gnu.org/pub/gcc/infrastructure/

  1. gmp-6.2.1
  2. mpfr-4.1.0
  3. mpc-1.2.1

Step 1. Install gmp-6.2.1

% bunzip2 gmp-6.2.1.tar.bz2
% tar -xvf gmp-6.2.1.tar
% cd gmp-6.2.1
% ./configure --prefix=/usr/local/gmp-6.2.1
% make 
% make install

Step 2: Install mpfr-4.1.0 (requires gmp-6.2.1 as prerequisites)

% bunzip2 mpfr-4.1.0.tar.bz
% tar -xvf mpfr-4.1.0.tar
% cd mpfr-4.1.0/
% ./configure --prefix=/usr/local/mpfr-4.1.0 --with-gmp=/usr/local/gmp-6.2.1/
% make
% make install

Step 3: Install mpc-1.2.1 (requires gmp-6.2.1 and mpfr-4.1.0)

% tar -zxvf mpc-1.2.1.tar.gz
% cd mpc-1.2.1/
% ./configure --prefix=/usr/local/mpc-1.2.1 -with-gmp=/usr/local/gmp-6.2.1 --with-mpfr=/usr/local/mpfr-4.1.0
% make
% make install

Step 4: Install isl-0.24 (requires gmp-6.2.1 as prerequisites)

% bunzip2 isl-0.24.tar.bz2
% tar -xvf isl-0.24.tar
% cd isl-0.24
% ./configure --prefix=/usr/local/isl-0.24 --with-gmp-prefix=/usr/local/gmp-6.2.1/
% make
% make install

Configure and Build GCC

% git clone git://gcc.gnu.org/git/gcc.git
% cd gcc
% mkdir build-gcc
% cd build-gcc
% ../configure --prefix=/usr/local/gcc-12.1 --enable-bootstrap --enable-languages=c,c++,fortran,lto --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux --with-static-standard-libraries --with-gmp=/usr/local/gmp-6.2.1 --with-mpc=/usr/local/mpc-1.2.1 --with-mpfr=/usr/local/mpfr-4.1.0 --with-isl=/usr/local/isl-0.24 --with-isl-lib=/usr/local/isl-0.24/lib --with-isl-include=/usr/local/isl-0.24/include

You may encounter issues like

/usr/local/software/gcc/build-gcc/./gcc/cc1: error while loading shared libraries: libisl.so.23: cannot open shared object file: No such file or directory

An alternative way is to let GCC do the download for you….. Retracing the steps 

% git clone git://gcc.gnu.org/git/gcc.git
% cd gcc
% contrib/download_prerequisites
% mkdir build-gcc
% cd build-gcc
% ../configure --prefix=/usr/local/gcc-12.1 --enable-bootstrap --enable-languages=c,c++,fortran,lto --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux --with-static-standard-libraries

If you encounter any errors during make such as 

/usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file or directory

It is due to missing glibc-devel and glibc-devel.i686. You have to do a dnf install glibc-devel and glibc-devel.i686

% dnf install glibc-devel glibc-devel.i686

References:

https://gcc.gnu.org/wiki/InstallingGCC

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Compiling LAMMPS-15Jun20 with GNU 6 and OpenMPI 3

Prerequisites

openmpi-3.1.4
gnu-6.5
m4-1.4.18
gmp-6.1.0
mpfr-3.1.4
mpc-1.0.3
isl-0.18
gsl-2.1
lammps-15Jun20

Download the latest tar.gz from https://lammps.sandia.gov/

Step 1: Untar LAMMPS

% tar -zxvf lammps-stable.tar.gz

Step 2: Go to $LAMMPS_HOME/src. Make Standard Packages

% cd src
% make yes-standard
% make no-gpu
% make no-mscg

Step 3: Compile message libraries

% cd lammps-15Jun20/lib/message/cslib/src
% make lib_parallel zmq=no

Copy and rename the produced cslib/src/libcsmpi.a or libscnompi.a file to cslib/src/libmessage.a

% cp cslib/src/libcsmpi.a cslib/src/libmessage.a

Copy either lammps-15Jun20/lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq to lib/message/Makefile.lammps

% cp Makefile.lammps.nozmq Makefile.lammps

Step 4: Compile poems

% cd lammps-15Jun20/lib/poems
% make -f Makefile.g++

Step 5: Compile latte
Download LATTE code and unpack the tarball either in this /lib/latte directory

% git clone https://github.com/lanl/LATTE

Inside lammps-15Jun20/lib/latte/LATTE
Modify the makefile.CHOICES according to your system architecture and compilers

% cd lammps-15Jun20/lib/latte/LATTE
% cp makefile.CHOICES makefile.CHOICES.gfort
% make
% cd lammps-15Jun20/lib/latte
% ln -s ./LATTE/src includelink
% ln -s ./LATTE liblink
% ln -s ./LATTE/src/latte_c_bind.o filelink.o
% cp Makefile.lammps.gfortran Makefile.lammps

Step 6. Compile Voronoi

Download voro++-0.4.6.tar.gz from http://math.lbl.gov/voro++/download/
Untar the voro++-0.4.6.tar.gz inside lammps-15Jun20/lib/voronoi/

% tar -zxvf voro++-0.4.6.tar.gz
% cd lammps-15Jun20/lib/voronoi/voro++-0.4.6
% make

Step 7: Compile kim

Download kim from https://openkim.org/doc/usage/obtaining-models . The current version is  kim-api-2.1.3.txz

Download at /lammps-15Jun20/lib/kim

% cd lammps-15Jun20/lib/kim
% tar Jxvf kim-api-2.1.3.txz
% cd kim-api-2.1.3
% mkdir build
% cd build
% cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-2.1.3
% make -j2
% make install
% cd /lammps-15Jun20/lib/kim/installed-kim-api-2.1.3/
% source ${PWD}/kim-api-X2.1.3/bin/kim-api-activate
% kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002

Step 8: Compile USER-COLVARS

% cd lammps-15Jun/lib/colvars
% make -f Makefile.g++

Step 9: Check Packages Status

% make package-status
[root@hpc-gekko1 src]# make package-status
Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed  NO: package GPU
Installed YES: package GRANULAR
Installed YES: package KIM
.....
.....

Step 9a: To Activate Standard Package

% make yes-standard

Step 9b: To activate USER-COLVARS, USER-OMP

% make yes-user-colvars
% make yes-user-omp

Step 9c: To deactivate GPGPU

% make no-gpu

Step 10: Finally Compile LAMMPS

% cd lammps-15Jun20/src
% make g++_openmpi -j 16

You should have binary called lmp_g++_openmpi
Do a softlink

ln -s lmp_g++_openmpi lammps
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Compiling OpenMPI-3.1.6 with GCC-6.5

We assumed that you have installed GNU 6.5 and isl-0.15

Download the latest OpenMPI 3.1.6 package from OpenMPI site

% ./configure --prefix=/usr/local/gnu/openmpi-3.1.6 --enable-orterun-prefix-by-default --enable-mpi-cxx --enable-openib-rdmacm-ibaddr --enable-mca-no-build=btl-uct

–enable-orterun-prefix-by-default (Configure OMPI –enable-orterun-prefix-by-default and so that you do not need to add the prefix option)
–enable-openib-rdmacm-ibaddr (To enable routing over IB)
–enable-mpi-cxx (C++ bindings are no more built by default)
–enable-mca-no-build=btl-uct (ecent OpenMPI versions contain a BTL component called ‘uct’, which can cause data corruption when enabled, due to conflict on malloc hooks between OPAL and UCM.)

% make all install | tee install.log

References:

  1. Intel Community – Caught Signal 11 (Segmentation Fault: Does not mapped to object at)
  2. Open MPI + Scalasca :Can not run mpirun command with option –prefix?