Hi Axel,
Thanks for the answers!
Concerning lammps-gui-build/cmake_install.cmake I did not make any change to it manually. It is the one created by cmake Since I am a new user of the forum, I cannot upload files, hence I incorporate it hereafter:
# Install script for directory: /usr/local/src/lammps-29Aug2024/tools/lammps-gui
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
set(CMAKE_INSTALL_PREFIX "/usr/local")
endif()
string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
# Set the install configuration name.
if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
if(BUILD_TYPE)
string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
else()
set(CMAKE_INSTALL_CONFIG_NAME "RelWithDebInfo")
endif()
message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
endif()
# Set the component getting installed.
if(NOT CMAKE_INSTALL_COMPONENT)
if(COMPONENT)
message(STATUS "Install component: \"${COMPONENT}\"")
set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
else()
set(CMAKE_INSTALL_COMPONENT)
endif()
endif()
# Install shared libraries without execute permission?
if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
set(CMAKE_INSTALL_SO_NO_EXE "1")
endif()
# Is this installation the result of a crosscompile?
if(NOT DEFINED CMAKE_CROSSCOMPILING)
set(CMAKE_CROSSCOMPILING "FALSE")
endif()
# Set default install directory permissions.
if(NOT DEFINED CMAKE_OBJDUMP)
set(CMAKE_OBJDUMP "/usr/bin/objdump")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui")
file(RPATH_CHECK
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui"
RPATH "")
endif()
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/usr/local/src/lammps-29Aug2024/build/lammps-gui")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui")
file(RPATH_CHANGE
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui"
OLD_RPATH "/opt/rocm-6.3.3/lib/llvm/lib:"
NEW_RPATH "")
if(CMAKE_INSTALL_DO_STRIP)
execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/lammps-gui")
endif()
endif()
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
include("/usr/local/src/lammps-29Aug2024/build/lammps-gui-build/CMakeFiles/lammps-gui.dir/install-cxx-module-bmi-RelWithDebInfo.cmake" OPTIONAL)
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/applications" TYPE FILE FILES "/usr/local/src/lammps-29Aug2024/tools/lammps-gui/lammps-gui.desktop")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/appdata" TYPE FILE FILES "/usr/local/src/lammps-29Aug2024/tools/lammps-gui/lammps-gui.appdata.xml")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/mime/packages" TYPE FILE FILES "/usr/local/src/lammps-29Aug2024/tools/lammps-gui/lammps-input.xml")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/mime/text/x-application-lammps.xml" TYPE FILE FILES "/usr/local/src/lammps-29Aug2024/tools/lammps-gui/lammps-input.xml")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/icons/" TYPE DIRECTORY FILES "/usr/local/src/lammps-29Aug2024/tools/lammps-gui/icons/hicolor")
endif()
if(CMAKE_INSTALL_COMPONENT STREQUAL "Unspecified" OR NOT CMAKE_INSTALL_COMPONENT)
file(GET_RUNTIME_DEPENDENCIES
LIBRARIES /usr/local/src/lammps-29Aug2024/build/liblammps.a
EXECUTABLES /usr/local/src/lammps-29Aug2024/build/lammps-gui /usr/local/src/lammps-29Aug2024/build/lmp
RESOLVED_DEPENDENCIES_VAR _r_deps
UNRESOLVED_DEPENDENCIES_VAR _u_deps
)
foreach(_file ${_r_deps})
file(INSTALL
DESTINATION "${CMAKE_INSTALL_PREFIX}/lib"
TYPE SHARED_LIBRARY
FOLLOW_SYMLINK_CHAIN
FILES "${_file}"
)
endforeach()
list(LENGTH _u_deps _u_length)
if("${_u_length}" GREATER 0)
message(WARNING "Unresolved dependencies detected: ${_u_deps}")
endif()
endif()
the output of sudo make -i install is the same as in my first message. The last lines are still:
CMake Error at lammps-gui-build/cmake_install.cmake:90 (file):
file unknown error.
Call Stack (most recent call first):
cmake_install.cmake:75 (include)
Concerning
ERROR: Floating point number 1.0 in input script or data file is invalid (src/lammps-29Aug2024/src/lattice.cpp:58)
I really do not understand it because I did not add any script name when I tried to launch lammps-gui:
(base) michel.devel@MN2S-DEVEL08:/usr/local/src/lammps-29Aug2024/build$ ./lammps-gui
LAMMPS (29 Aug 2024 - Update 1)
using 24 OpenMP thread(s) per MPI task
ERROR: Floating point number 1.0 in input script or data file is invalid (src/lammps-29Aug2024/src/lattice.cpp:58)
Last command: (unknown)
LAMMPS Exception: ERROR: Floating point number 1.0 in input script or data file is invalid (src/lammps-29Aug2024/src/lattice.cpp:58)
For /usr/local/bin/lammps-gui I first got
/usr/local/bin/lammps-gui: error while loading shared libraries: libomp.so: cannot open shared object file: No such file or directory
Then I did export LD_LIBRARY_PATH=/opt/rocm/lib/llvm/lib:$LD_LIBRARY_PATH and then
/usr/local/bin/lammps-gui gave me exactly the same error message as above for ./lammps-gui in the build folderâŚ
Concerning the output of ldd /usr/local/bin/lammps-gui, here it is:
linux-vdso.so.1 (0x00007ffd0d5ad000)
libQt5Charts.so.5 => /lib/x86_64-linux-gnu/libQt5Charts.so.5 (0x00007faa47c7b000)
libcurl-gnutls.so.4 => /lib/x86_64-linux-gnu/libcurl-gnutls.so.4 (0x00007faa47bc0000)
libjpeg.so.8 => /lib/x86_64-linux-gnu/libjpeg.so.8 (0x00007faa47b3d000)
libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007faa45600000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faa47a52000)
libgsl.so.27 => /lib/x86_64-linux-gnu/libgsl.so.27 (0x00007faa45200000)
libgslcblas.so.0 => /lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007faa47a12000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007faa479f6000)
libfftw3.so.3 => /lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007faa44e00000)
libomp.so => /opt/rocm/lib/llvm/lib/libomp.so (0x00007faa45506000)
libamdhip64.so.6 => /opt/rocm-6.3.3/lib/llvm/bin/../../../lib/libamdhip64.so.6 (0x00007faa43600000)
libQt5Widgets.so.5 => /lib/x86_64-linux-gnu/libQt5Widgets.so.5 (0x00007faa42e00000)
libQt5Gui.so.5 => /lib/x86_64-linux-gnu/libQt5Gui.so.5 (0x00007faa42600000)
libQt5Core.so.5 => /lib/x86_64-linux-gnu/libQt5Core.so.5 (0x00007faa42000000)
libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007faa41c00000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007faa454d8000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faa41800000)
/lib64/ld-linux-x86-64.so.2 (0x00007faa47e64000)
libnghttp2.so.14 => /lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007faa454ad000)
libidn2.so.0 => /lib/x86_64-linux-gnu/libidn2.so.0 (0x00007faa451de000)
librtmp.so.1 => /lib/x86_64-linux-gnu/librtmp.so.1 (0x00007faa451c0000)
libssh.so.4 => /lib/x86_64-linux-gnu/libssh.so.4 (0x00007faa4514f000)
libpsl.so.5 => /lib/x86_64-linux-gnu/libpsl.so.5 (0x00007faa479dc000)
libnettle.so.8 => /lib/x86_64-linux-gnu/libnettle.so.8 (0x00007faa450fa000)
libgnutls.so.30 => /lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007faa41606000)
libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007faa450a6000)
libldap.so.2 => /lib/x86_64-linux-gnu/libldap.so.2 (0x00007faa45048000)
liblber.so.2 => /lib/x86_64-linux-gnu/liblber.so.2 (0x00007faa45036000)
libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00007faa44d46000)
libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007faa45028000)
libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007faa41200000)
librocprofiler-register.so.0 => /opt/rocm-6.3.3/lib/llvm/bin/../../../lib/librocprofiler-register.so.0 (0x00007faa44cc1000)
libamd_comgr.so.2 => /opt/rocm-6.3.3/lib/llvm/bin/../../../lib/libamd_comgr.so.2 (0x00007faa38600000)
libhsa-runtime64.so.1 => /opt/rocm-6.3.3/lib/llvm/bin/../../../lib/libhsa-runtime64.so.1 (0x00007faa38200000)
libnuma.so.1 => /lib/x86_64-linux-gnu/libnuma.so.1 (0x00007faa44cb3000)
libGL.so.1 => /lib/x86_64-linux-gnu/libGL.so.1 (0x00007faa43579000)
libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00007faa44c7b000)
libharfbuzz.so.0 => /lib/x86_64-linux-gnu/libharfbuzz.so.0 (0x00007faa41ef3000)
libmd4c.so.0 => /lib/x86_64-linux-gnu/libmd4c.so.0 (0x00007faa43567000)
libdouble-conversion.so.3 => /lib/x86_64-linux-gnu/libdouble-conversion.so.3 (0x00007faa43552000)
libicui18n.so.74 => /lib/x86_64-linux-gnu/libicui18n.so.74 (0x00007faa37e00000)
libicuuc.so.74 => /lib/x86_64-linux-gnu/libicuuc.so.74 (0x00007faa37a00000)
libpcre2-16.so.0 => /lib/x86_64-linux-gnu/libpcre2-16.so.0 (0x00007faa434c6000)
libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007faa41ab7000)
libunistring.so.5 => /lib/x86_64-linux-gnu/libunistring.so.5 (0x00007faa37c53000)
libhogweed.so.6 => /lib/x86_64-linux-gnu/libhogweed.so.6 (0x00007faa42db8000)
libgmp.so.10 => /lib/x86_64-linux-gnu/libgmp.so.10 (0x00007faa42d34000)
libcrypto.so.3 => /lib/x86_64-linux-gnu/libcrypto.so.3 (0x00007faa37400000)
libp11-kit.so.0 => /lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007faa3725c000)
libtasn1.so.6 => /lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007faa42d1e000)
libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007faa4153d000)
libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007faa425d4000)
libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007faa44c71000)
libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007faa42d11000)
libsasl2.so.2 => /lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007faa425ba000)
libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007faa42597000)
libelf.so.1 => /lib/x86_64-linux-gnu/libelf.so.1 (0x00007faa42578000)
libdrm.so.2 => /opt/amdgpu/lib/x86_64-linux-gnu/libdrm.so.2 (0x00007faa42cf8000)
libdrm_amdgpu.so.1 => /opt/amdgpu/lib/x86_64-linux-gnu/libdrm_amdgpu.so.1 (0x00007faa41ee4000)
libGLdispatch.so.0 => /lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007faa41148000)
libGLX.so.0 => /lib/x86_64-linux-gnu/libGLX.so.0 (0x00007faa41eb1000)
libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007faa37934000)
libgraphite2.so.3 => /lib/x86_64-linux-gnu/libgraphite2.so.3 (0x00007faa41e8b000)
libicudata.so.74 => /lib/x86_64-linux-gnu/libicudata.so.74 (0x00007faa35400000)
libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007faa41a1d000)
libffi.so.8 => /lib/x86_64-linux-gnu/libffi.so.8 (0x00007faa41e7f000)
libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007faa434bd000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007faa4152a000)
libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007faa352c3000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007faa41134000)
libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x00007faa4110b000)
libXau.so.6 => /lib/x86_64-linux-gnu/libXau.so.6 (0x00007faa41a17000)
libXdmcp.so.6 => /lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007faa41522000)
libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007faa410f5000)
libmd.so.0 => /lib/x86_64-linux-gnu/libmd.so.0 (0x00007faa410e6000)
Concerning the reasons of my using sudo, it is because I want to install the same version of LAMMPS for all the users of that machine (people from my group), not only me.
Furthermore, I did not want to use a pre-compiled binary because I think I have been using lammps for more than a decade now and some times I was missing some package e.g. in the Windows version (which was nonetheless very useful for internships or for hands on classes when I was teaching Molecular Dynamics to beginners for example) or even in the linux version. Hence I have experiment in compling LAMMPS from source and chosing the packages I want to add and do not mind doing it. This time, it is because of the use of GPU version with my particular GPU and also because of the EXTRA-FIX package.
Finally, I must admit that I do not understand why using MPI instead of OpenMP would be more efficient on our single node machine with only one CPU and one GPU, but I am ready to learn why and change my mind! 
Thanks again for your help,
Michel DEVEL