now molscat can be built using cmake
This commit is contained in:
parent
06b83b1561
commit
f4abe26b1f
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@ -0,0 +1,215 @@
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# CMake project file for molscat
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cmake_minimum_required (VERSION 3.13)
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project (molscat VERSION 14.0)
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enable_language (Fortran)
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message("Fortran compiler ID: ${CMAKE_Fortran_COMPILER_ID}")
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# get in Fortran_COMPILER_NAME the name of the compiler (eg ifx)
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get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
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message("Fortran compiler: ${Fortran_COMPILER_NAME}")
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find_package( BLAS REQUIRED )
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find_package( LAPACK REQUIRED )
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message(STATUS "BLAS_LIBRARIES = ${BLAS_LIBRARIES}")
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message(STATUS "LAPACK_LIBRARIES = ${LAPACK_LIBRARIES}")
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add_executable(molscat
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potenl_pes.f
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POTEN_rigidXD.f90
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SUBROUTINES_F77.f
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v14_new.f
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vrtp_co_co2.f
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)
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################################################################################
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#
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# COMPILE OPTIONS
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#
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################################################################################
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# GNU (gfortran)
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if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
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target_compile_options(molscat
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PUBLIC
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# Non-specific options
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-std=legacy # Allow pre-Fortran 77 syntax (e.g. arbitrary length arrays)
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-ffree-line-length-none # Allow arbitrary long lines. Needed as preprocessing could generate long line lengths.
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# -fdefault-integer-8
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# -finteger-4-integer-8
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$<$<BOOL:${SAVE}>:-fno-automatic> # Put local variables on the heap instead of the stack. As a side effect, all affected variables receive the save attribute (persistance between calls). This flag conflicts with -fopenmp (f951: Warning: Flag ‘-fno-automatic’ overwrites ‘-frecursive’ implied by ‘-fopenmp’)
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$<$<PLATFORM_ID:Linux>:-mcmodel=large> # Required on Linux
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$<$<BOOL:${OpenMP_Fortran_FOUND}>:-fopenmp> # Compile with fopenmp option if OpenMP libs are found
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# Config-specific options: RELEASE
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$<$<CONFIG:RELEASE>:-O3> # Optimization level at 3 for Release
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$<$<AND:$<BOOL:${LINK_TIME_OPTIMIZATION}>,$<CONFIG:RELEASE>>:-flto> # Activate link time optimizations so that gfortran can inline some function calls
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#$<$<CONFIG:RELEASE>:-fopt-info> # You can get some information from gfortran with the flag -fopt-info that will tell you about optimizations missed or performed by the compiler
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$<$<CONFIG:RELEASE>:-finit-local-zero> # Init variables to zero/false/null
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# Config-specific options: DEBUG
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$<$<CONFIG:DEBUG>:-O0> # Optimization level at 0
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$<$<CONFIG:DEBUG>:-g> # Include symbols in executable for easier debugging
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$<$<CONFIG:DEBUG>:-fno-omit-frame-pointer>
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$<$<CONFIG:DEBUG>:-fbacktrace> # Generates extra information in the object file to provide source file traceback information when a severe error occurs at run time
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$<$<CONFIG:DEBUG>:-Wall> # Enable all warnings
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$<$<CONFIG:DEBUG>:-Wextra> # Enable extra warnings
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$<$<CONFIG:DEBUG>:-Wno-conversion> # Disable warnings such as Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
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$<$<CONFIG:DEBUG>:-Wno-compare-reals> # Disable warnings such as "Warning: Equality comparison for REAL(8) at (1) [-Wcompare-reals]" as they are often fine when comparing with 2 hardcoded zero constants
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$<$<CONFIG:DEBUG>:-fsanitize=address> # Address sanitizer
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$<$<AND:$<NOT:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>>,$<CONFIG:DEBUG>>:-Wuninitialized> # Emit warnings for uninitialized variables. Disable -Wuninitialized when ENABLE_UNINIT_VAR_RUNTIME_DETECTOR is on because the the -finit-* options then used make -Wuninitialized have no effect, see gfortran documentation :
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# Finally, note that enabling any of the -finit-* options will silence warnings that would have been emitted by -Wuninitialized for the affected local variables.
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# handle ENABLE_UNINIT_VAR_RUNTIME_DETECTOR
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# don't initialize local variables to zero : initialize them with dummy values to force failures which help detect uninitialized variables as -Wuninitialized doesn't detect everything (see issue #38 or https://stackoverflow.com/questions/39591300/gfortran-wuninitialized-flag-misses-variable-in-do-loop)
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# by default, gfortran initializes integers to 0, but not ifort : as a result, some bugs in the code are hidden with gfortran default options
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# set (CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fno-init-local-zero")
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# initialize variables to something else than 0 to force the programe to behave badly in case of unitialized variables
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-finit-integer=333333333>
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-finit-real=snan>
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-ffpe-trap=invalid,zero,overflow>
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# The --coverage option of the Gcc compiler, which is synonymous with -fprofile-arcs and -ftest-coverage for compilation and -lgcov for linking, allows the generation of code coverage data files after program execution. After tests performed with Check, the test executable produces a .gcno (Gcov notes) file and a .gcda (Gcov data) file for each file compiled with the -fprofile-arcs option and used during the test (see gcc manual).
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# These files are then used by the lcov tool to produce a code coverage report in HTML format.
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$<$<BOOL:${ENABLE_CODE_COVERAGE}>:--coverage -Wno-coverage-invalid-line-number> # Code coverage (same as -fprofile-arcs -ftest-coverage at compile time)
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$<$<BOOL:${ENABLE_PROFILING}>:-g> # The profiler requires both the debug and profile directives (-g and -p)
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$<$<BOOL:${ENABLE_PROFILING}>:-p> # The profiler requires both the debug and profile directives (-g and -p)
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)
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# Intel (ifort)
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elseif (Fortran_COMPILER_NAME STREQUAL "ifort")
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target_compile_options(molscat
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PUBLIC
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# Non-specific options
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# force arrays to be allocated on the heap instead of the stack, this removes segmentation faults crash, not sure why
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# the following option means : automatic arrays and arrays created for temporary computations are allocated on the stack if their size can be determined at compile time and if it doesn't exceed 10kb.
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# this option seems necessary for big values of kmax (eg kmax=5000), according to bdesrousseaux, otherwise the user will experience a segmentation fault. I guess that without this option, the stack becomes too small to contain such big arrays...
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-heap-arrays # Put everything on the heap
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# "-extend-source 132" # Allow arbitrary long lines (132 seems the longest allowed with ifort). Needed as preprocessing could generate long lines.
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-no-wrap-margin # Don't wrap output files
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$<$<PLATFORM_ID:Linux>:-mcmodel=large> # Required on Linux
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$<$<BOOL:${OpenMP_Fortran_FOUND}>:-qopenmp> # Compile with qopenmp option if OpenMP libs are found
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# Config-specific options: RELEASE
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$<$<CONFIG:RELEASE>:-O3> # Optimization level at 3 for Release
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$<$<AND:$<BOOL:${LINK_TIME_OPTIMIZATION}>,$<CONFIG:RELEASE>>:-ipo> # activate interprocediral optimization (aka link time optimization)
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$<$<CONFIG:RELEASE>:-init=zero> # Init variables to zero/false/null
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# Config-specific options: DEBUG
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$<$<CONFIG:DEBUG>:-O0> # Disable all optimizations
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$<$<CONFIG:DEBUG>:-g> # Generates complete debugging information
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$<$<CONFIG:DEBUG>:-traceback> # Generates extra information in the object file to provide source file traceback information when a severe error occurs at run time
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$<$<CONFIG:DEBUG>:-fp-stack-check> # Tell the compiler to generate extra code after every function call to ensure that the floating-point stack is in the expected state
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#$<$<CONFIG:DEBUG>:-warn all> # Enable all warnings
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# handle ENABLE_UNINIT_VAR_RUNTIME_DETECTOR
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# Force à NaN toutes les variables de type intrinsèque ainsi que les tableaux non initialisés. Cette option implique -fpe0. Pour éviter de récupérer des exceptions, qui ne soient pas relatives à des variables non-initialisées, nous recommandons de réduire le niveau d'optimisation à -O1 ou -O0 ou alors d'utiliser -fp-speculation=safe pour faire la détection de variables non-initialisés.
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=zero> # Init integer and logical variables to zero/false/null instead of random to avoid random bugs
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=snan> # Init real variables to signaling nans to detect uninitialized variables
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=arrays> # also initialize arrays to avoid random behaviours caused by use of uninitialized variables
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# check uses of uninitialized variables in run time
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# this is very useful as these are always bugs that cause the program to behave randomly with ifort (gfortran initializes data with zero)
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-check uninit>
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# Cette combinaison d'options stoppe l'exécution dès qu'une exception (overflow, underflow, division par zéro, opération invalide,…) se produit; elle indique à quel niveau du code elle s'est produite. Le contrôle s'opère dans chaque subroutine, contrairement à l'option -fpe0 qui agit uniquement sur le programme principal.
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-fpe-all=0>
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-no-ftz=0>
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-traceback=0>
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$<$<BOOL:${ENABLE_PROFILING}>:-g> # The profiler requires both the debug and profile directives (-g and -p)
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$<$<BOOL:${ENABLE_PROFILING}>:-p> # The profiler requires both the debug and profile directives (-g and -p)
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-diag-disable 6717,7712 # disable warning #6717 (This name has not been given an explicit type. [LMAXP]) until all variables have been declared explicitely (implicit None)
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# -diag-disable 7712 # disable remark #7712: This variable has not been used. until all variables have been declared explicitely (implicit None)
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$<$<CONFIG:DEBUG>:-warn all,nounused,nodeclarations,errors> # Enable all warnings except for some that have not been fixed yet, and treat warnings as errors for a zero warning policy
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)
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# Intel (Fortran_COMPILER_NAME=ifx, Fortran_COMPILER_ID=IntelLLVM)
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elseif (Fortran_COMPILER_NAME STREQUAL "ifx")
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target_compile_options(molscat
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PUBLIC
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# Non-specific options
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# force arrays to be allocated on the heap instead of the stack, this removes segmentation faults crash, not sure why
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# the following option means : automatic arrays and arrays created for temporary computations are allocated on the stack if their size can be determined at compile time and if it doesn't exceed 10kb.
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# this option seems necessary for big values of kmax (eg kmax=5000), according to bdesrousseaux, otherwise the user will experience a segmentation fault. I guess that without this option, the stack becomes too small to contain such big arrays...
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-heap-arrays # Put everything on the heap
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# "-extend-source 132" # Allow arbitrary long lines (132 seems the longest allowed with ifort). Needed as preprocessing could generate long lines.
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-no-wrap-margin # Don't wrap output files
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$<$<PLATFORM_ID:Linux>:-mcmodel=large> # Required on Linux
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$<$<BOOL:${OpenMP_Fortran_FOUND}>:-qopenmp> # Compile with qopenmp option if OpenMP libs are found
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# Config-specific options: RELEASE
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$<$<CONFIG:RELEASE>:-O3> # Optimization level at 3 for Release
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$<$<AND:$<BOOL:${LINK_TIME_OPTIMIZATION}>,$<CONFIG:RELEASE>>:-ipo> # activate interprocediral optimization (aka link time optimization)
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$<$<CONFIG:RELEASE>:-init=zero> # Init variables to zero/false/null
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# Config-specific options: DEBUG
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$<$<CONFIG:DEBUG>:-O0> # Disable all optimizations
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$<$<CONFIG:DEBUG>:-g> # Generates complete debugging information
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$<$<CONFIG:DEBUG>:-traceback> # Generates extra information in the object file to provide source file traceback information when a severe error occurs at run time
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#$<$<CONFIG:DEBUG>:-warn all> # Enable all warnings
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# handle ENABLE_UNINIT_VAR_RUNTIME_DETECTOR
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# Force à NaN toutes les variables de type intrinsèque ainsi que les tableaux non initialisés. Cette option implique -fpe0. Pour éviter de récupérer des exceptions, qui ne soient pas relatives à des variables non-initialisées, nous recommandons de réduire le niveau d'optimisation à -O1 ou -O0 ou alors d'utiliser -fp-speculation=safe pour faire la détection de variables non-initialisés.
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=zero> # Init integer and logical variables to zero/false/null instead of random to avoid random bugs
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=snan> # Init real variables to signaling nans to detect uninitialized variables
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-init=arrays> # also initialize arrays to avoid random behaviours caused by use of uninitialized variables
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# check uses of uninitialized variables in run time
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# this is very useful as these are always bugs that cause the program to behave randomly with ifort (gfortran initializes data with zero)
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-check uninit>
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# Cette combinaison d'options stoppe l'exécution dès qu'une exception (overflow, underflow, division par zéro, opération invalide,…) se produit; elle indique à quel niveau du code elle s'est produite. Le contrôle s'opère dans chaque subroutine, contrairement à l'option -fpe0 qui agit uniquement sur le programme principal.
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-fpe-all=0>
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-no-ftz=0>
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# $<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-traceback=0>
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$<$<BOOL:${ENABLE_PROFILING}>:-g> # The profiler requires both the debug and profile directives (-g and -p)
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$<$<BOOL:${ENABLE_PROFILING}>:-p> # The profiler requires both the debug and profile directives (-g and -p)
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-diag-disable 6717,7712 # disable warning #6717 (This name has not been given an explicit type. [LMAXP]) until all variables have been declared explicitely (implicit None)
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# -diag-disable 7712 # disable remark #7712: This variable has not been used. until all variables have been declared explicitely (implicit None)
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$<$<CONFIG:DEBUG>:-warn all,nounused,nodeclarations,errors> # Enable all warnings except for some that have not been fixed yet, and treat warnings as errors for a zero warning policy
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)
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else()
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message(FATAL_ERROR "Unsupported Fortran compiler: ${CMAKE_Fortran_COMPILER_ID} (${Fortran_COMPILER_NAME})")
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endif()
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################################################################################
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#
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# LINK OPTIONS
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#
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################################################################################
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# Link Blas and Lapack libraries
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if(Fortran_COMPILER_NAME STREQUAL "ifx")
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if(BLA_VENDOR STREQUAL "Intel10_64lp")
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# -- BLAS_LIBRARIES = /opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_intel_lp64.so;/opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_intel_thread.so;/opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_core.so;/opt/intel/oneapi-2024.2.1/compiler/2024.2/lib/libiomp5.so;-lm;-ldl
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# -- LAPACK_LIBRARIES = /opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_intel_lp64.so;/opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_intel_thread.so;/opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_core.so;/opt/intel/oneapi-2024.2.1/compiler/2024.2/lib/libiomp5.so;-lm;-ldl;-lm;-ldl
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# in this case, BLAS_LIBRARIES and LAPACK_LIBRARIES are the same, and linking bith would cause ifx to faiol with the error:
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# "ld: attempted static link of dynamic object `/opt/intel/oneapi-2024.2.1/mkl/2024.2/lib/libmkl_intel_lp64.so'
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target_link_libraries(molscat PUBLIC "${BLAS_LIBRARIES}")
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else()
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target_link_libraries(molscat PUBLIC "${BLAS_LIBRARIES}")
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target_link_libraries(molscat PUBLIC "${LAPACK_LIBRARIES}")
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endif()
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else()
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target_link_libraries(molscat PUBLIC "${BLAS_LIBRARIES}")
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target_link_libraries(molscat PUBLIC "${LAPACK_LIBRARIES}")
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endif()
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# GNU (gfortran)
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if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
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target_link_libraries(molscat
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PUBLIC
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$<$<CONFIG:DEBUG>:-fsanitize=address> # Address sanitizer (beware: tests showed that with -fsanitize=address memory is not actually released when deallocate is called. Is this a true memory leak in address sanitizer?)
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)
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# Intel (ifort)
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elseif (Fortran_COMPILER_NAME STREQUAL "ifort")
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endif()
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# GNU (gfortran)
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if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
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target_link_options(molscat
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PUBLIC
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$<$<CONFIG:DEBUG>:-fsanitize=address> # Address sanitizer
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$<$<BOOL:${ENABLE_CODE_COVERAGE}>:--coverage> # Code coverage (same as -lgcov at link time)
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)
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elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "IntelLLVM") # Intel (ifx)
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target_link_options(molscat
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PUBLIC
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$<$<AND:$<BOOL:${ENABLE_UNINIT_VAR_RUNTIME_DETECTOR}>,$<CONFIG:DEBUG>>:-check uninit> # https://community.intel.com/t5/Intel-Fortran-Compiler/Linking-errors-when-using-memory-sanitizer-in-fortran-project/td-p/1521476: When you compile with -check uninit (or -check all) you also need to link with that compiler option.
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)
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endif()
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89
readme.md
89
readme.md
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@ -3,7 +3,94 @@ This is molscat 14 modified by F. Lique
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## how to build
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```sh
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gfortran -o molscat -std=legacy -mcmodel=large *.f *.f90
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graffy@graffy-ws2:~/work/saboi$ ls -l
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total 4
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drwxr-xr-x 3 graffy spm 4096 févr. 20 13:51 molscat_14.git
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```
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create a directory for the build:
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```sh
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graffy@graffy-ws2:~/work/saboi$ mkdir molscat_14.build
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graffy@graffy-ws2:~/work/saboi$ cd molscat_14.build/
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```
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configure the build
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```sh
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graffy@graffy-ws2:~/work/saboi/molscat_14.build$ cmake ../molscat_14.git/
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-- The C compiler identification is GNU 9.4.0
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-- The CXX compiler identification is GNU 9.4.0
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-- Check for working C compiler: /usr/bin/cc
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-- Check for working C compiler: /usr/bin/cc -- works
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-- Detecting C compiler ABI info
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-- Detecting C compiler ABI info - done
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-- Detecting C compile features
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-- Detecting C compile features - done
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-- Check for working CXX compiler: /usr/bin/c++
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-- Check for working CXX compiler: /usr/bin/c++ -- works
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-- Detecting CXX compiler ABI info
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-- Detecting CXX compiler ABI info - done
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-- Detecting CXX compile features
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-- Detecting CXX compile features - done
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-- The Fortran compiler identification is GNU 9.4.0
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-- Check for working Fortran compiler: /usr/bin/gfortran
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-- Check for working Fortran compiler: /usr/bin/gfortran -- works
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-- Detecting Fortran compiler ABI info
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-- Detecting Fortran compiler ABI info - done
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-- Checking whether /usr/bin/gfortran supports Fortran 90
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-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
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Fortran compiler ID: GNU
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Fortran compiler: gfortran
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-- Looking for Fortran sgemm
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-- Looking for Fortran sgemm - not found
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-- Looking for pthread.h
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-- Looking for pthread.h - found
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-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
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-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
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-- Looking for pthread_create in pthreads
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-- Looking for pthread_create in pthreads - not found
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-- Looking for pthread_create in pthread
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-- Looking for pthread_create in pthread - found
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-- Found Threads: TRUE
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-- Looking for Fortran sgemm
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-- Looking for Fortran sgemm - found
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-- Found BLAS: /usr/lib/x86_64-linux-gnu/libopenblas.so
|
||||
-- Looking for Fortran cheev
|
||||
-- Looking for Fortran cheev - found
|
||||
-- A library with LAPACK API found.
|
||||
-- BLAS_LIBRARIES = /usr/lib/x86_64-linux-gnu/libopenblas.so
|
||||
-- LAPACK_LIBRARIES = /usr/lib/x86_64-linux-gnu/libopenblas.so
|
||||
-- Configuring done
|
||||
-- Generating done
|
||||
-- Build files have been written to: /home/graffy/work/saboi/molscat_14.build
|
||||
```
|
||||
|
||||
This created the makefile [~/work/saboi/molscat_14.build/Makefile].
|
||||
|
||||
Build the `moscat` executable using the makefile [~/work/saboi/molscat_14.build/Makefile]
|
||||
|
||||
```sh
|
||||
graffy@graffy-ws2:~/work/saboi/molscat_14.build$ make
|
||||
Scanning dependencies of target molscat
|
||||
[ 16%] Building Fortran object CMakeFiles/molscat.dir/POTEN_rigidXD.f90.o
|
||||
[ 33%] Building Fortran object CMakeFiles/molscat.dir/potenl_pes.f.o
|
||||
[ 50%] Building Fortran object CMakeFiles/molscat.dir/SUBROUTINES_F77.f.o
|
||||
[ 66%] Building Fortran object CMakeFiles/molscat.dir/v14_new.f.o
|
||||
/home/graffy/work/saboi/molscat_14.git/v14_new.f:10033:10:
|
||||
|
||||
10031 | DO 21 IM2=2,NMID
|
||||
| 2
|
||||
...
|
||||
Warning: Named COMMON block ‘cmbase’ at (1) shall be of the same size as elsewhere (24248 vs 24256 bytes)
|
||||
/home/graffy/work/saboi/molscat_14.git/v14_new.f:11:21:
|
||||
|
||||
11 | COMMON /MEMORY/ MX,IXNEXT,NIPR,IVLFL,X
|
||||
| 1
|
||||
Warning: Named COMMON block ‘memory’ at (1) shall be of the same size as elsewhere (800000016 vs 24 bytes)
|
||||
[ 83%] Building Fortran object CMakeFiles/molscat.dir/vrtp_co_co2.f.o
|
||||
[100%] Linking Fortran executable molscat
|
||||
[100%] Built target molscat
|
||||
```
|
||||
|
||||
## how to run
|
||||
|
|
|
|||
Loading…
Reference in New Issue