# CMake project file for cluster analysis from WHAM for oligomeric proteins
#
-enable_language (Fortran)
+enable_language (Fortran C)
#================================
# Set source file lists
rescode.f
setup_var.f
srtclust.f
+ ssMD.F
timing.F
track.F
wrtclust.f
probabl.F
read_coords.F
readrtns.F
+ ssMD.F
timing.F
track.F
work_partition.F
- proc_proc.c
)
# Set comipiler flags for different sourcefiles
#================================================
if (Fortran_COMPILER_NAME STREQUAL "ifort")
- set(FFLAGS0 "-ip -w -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres " )
+ set(FFLAGS0 "-mcmodel=medium -shared-intel -ip -w -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(FFLAGS0 "-I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres " )
+ set(FFLAGS0 "-std=legacy -mcmodel=medium -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+else ()
+ set(FFLAGS0 "-I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
+#=========================================
# Add MPI compiler flags
+#=========================================
if(UNRES_WITH_MPI)
- set(FFLAGS0 "${FFLAGS0} -I${MPIF_INCLUDE_DIRECTORIES}")
+ set(FFLAGS0 "${FFLAGS0} -I${MPI_Fortran_INCLUDE_PATH}")
endif(UNRES_WITH_MPI)
set_property(SOURCE ${UNRES_CLUSTER_WHAM_M_SRC0} PROPERTY COMPILE_FLAGS ${FFLAGS0} )
-set(CPPFLAGS "PROCOR -DSPLITELE -DPROCOR -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+#=========================================
+# Settings for GAB force field
+#=========================================
+if(UNRES_MD_FF STREQUAL "GAB" )
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DSPLITELE -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
+
+#=========================================
+# Settings for E0LL2Y force field
+#=========================================
+elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DSPLITELE -DSCCORPDB" )
+elseif(UNRES_MD_FF STREQUAL "4P")
+ set(CPPFLAGS "SPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
+endif(UNRES_MD_FF STREQUAL "GAB")
+
+#=========================================
+# Additional flags
+#=========================================
+set(CPPFLAGS "${CPPFLAGS} -DUNRES -DISNAN")
+#=========================================
+# Compiler specific flags
+#=========================================
if (Fortran_COMPILER_NAME STREQUAL "ifort")
# Add ifort preprocessor flags
set(CPPFLAGS "${CPPFLAGS} -DPGI")
#=========================================
set_property(SOURCE ${UNRES_CLUSTER_WHAM_M_PP_SRC} PROPERTY COMPILE_DEFINITIONS ${CPPFLAGS} )
+set_property(SOURCE proc_proc.c PROPERTY COMPILE_DEFINITIONS "LINUX -DPGI" )
#========================================
# Setting binary name
#========================================
-set(UNRES_CLUSTER_WHAM_M_BIN "unres_clustMD.exe")
+set(UNRES_CLUSTER_WHAM_M_BIN "cluster_wham-mult_${Fortran_COMPILER_NAME}_MPI_${UNRES_MD_FF}.exe")
#=========================================
-# cinfo.f stupid workaround for cmake
-# - shame on me ]:)
+# cinfo.f workaround for CMake
#=========================================
-#set_property(SOURCE compinfo.c PROPERTY CMAKE_C_FLAGS "-c" )
-#add_executable(compinfo-wham-m compinfo.c)
-#set_target_properties(compinfo-wham-m PROPERTIES OUTPUT_NAME compinfo)
+# get the current date
+TODAY(DATE)
+# generate cinfo.f
+
+set(CINFO "${CMAKE_CURRENT_BINARY_DIR}/cinfo.f")
+FILE(WRITE ${CINFO}
+"C CMake generated file
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version ${UNRES_MAJOR}.${UNRES_MINOR} build ${UNRES_PATCH}'
+")
+
+CINFO_FORMAT(${CINFO} "Compiled" "${DATE}" )
+CINFO_FORMAT(${CINFO} "Compiled by" "$ENV{USER}@$ENV{HOST}" )
+CINFO_FORMAT(${CINFO} "OS name:" "${CMAKE_SYSTEM_NAME}" )
+CINFO_FORMAT(${CINFO} "OS release:" "${CMAKE_SYSTEM}" )
+CINFO_FORMAT(${CINFO} "Fortran Compiler:" "${CMAKE_Fortran_COMPILER}" )
+CINFO_FORMAT(${CINFO} "MD Force field:" "${UNRES_MD_FF}" )
+CINFO_FORMAT(${CINFO} "CPPFLAGS =" "${CPPFLAGS}")
+
+FILE(APPEND ${CINFO}
+" write(iout,*)'++++ End of compile info ++++'
+ return
+ end ")
+
+# set include path
+set_property(SOURCE ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f PROPERTY COMPILE_FLAGS "${FFLAGS0} -I${CMAKE_CURRENT_SOURCE_DIR}" )
+
+
+set_property(SOURCE proc_proc.c PROPERTY COMPILE_DEFINITIONS "LINUX -DPGI" )
-#set(UNRES_CINFO_DIR "${CMAKE_CURRENT_BINARY_DIR}" )
-#add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
-# COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/cinfo.f ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
-# COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/COMMON.IOUNITS ${CMAKE_CURRENT_BINARY_DIR}/COMMON.IOUNITS
-# COMMAND ${CMAKE_CURRENT_BINARY_DIR}/compinfo | true
-# DEPENDS compinfo-wham-m )
-#set_property(SOURCE ${UNRES_CINFO_DIR}/cinfo.f PROPERTY COMPILE_FLAGS ${FFLAGS0} )
#=========================================
# Set full unres CLUSTER sources
#=========================================
-set(UNRES_CLUSTER_WHAM_M_SRCS ${UNRES_CLUSTER_WHAM_M_SRC0} ${CMAKE_CURRENT_SOURCE_DIR}/proc_proc.c)
+set(UNRES_CLUSTER_WHAM_M_SRCS ${UNRES_CLUSTER_WHAM_M_SRC0} ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f proc_proc.c)
#=========================================
# Build the binary
#=========================================
add_executable(UNRES_CLUSTER_WHAM_M_BIN ${UNRES_CLUSTER_WHAM_M_SRCS} )
set_target_properties(UNRES_CLUSTER_WHAM_M_BIN PROPERTIES OUTPUT_NAME ${UNRES_CLUSTER_WHAM_M_BIN})
+set_property(TARGET UNRES_CLUSTER_WHAM_M_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
#=========================================
# Link libraries
#=========================================
-# link MPI library (libmpich.a)
+# link MPI libraries
if(UNRES_WITH_MPI)
- target_link_libraries( UNRES_CLUSTER_WHAM_M_BIN ${MPIF_LIBRARIES} )
+ target_link_libraries( UNRES_CLUSTER_WHAM_M_BIN ${MPI_Fortran_LIBRARIES} )
endif(UNRES_WITH_MPI)
# link libxdrf.a
target_link_libraries( UNRES_CLUSTER_WHAM_M_BIN xdrf )
+
#=========================================
-# TESTS
+# Install Path
#=========================================
+install(TARGETS UNRES_CLUSTER_WHAM_M_BIN DESTINATION ${CMAKE_INSTALL_PREFIX}/cluster)
-#-- Copy all the data files from the test directory into the source directory
-#SET(UNRES_TEST_FILES
-# ala10.inp
-# )
-
-#FOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
-# SET (unres_test_dest "${CMAKE_CURRENT_BINARY_DIR}/${UNRES_TEST_FILE}")
-# MESSAGE (STATUS " Copying ${UNRES_TEST_FILE} from ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} to ${unres_test_dest}")
-# ADD_CUSTOM_COMMAND (
-# TARGET ${UNRES_BIN}
-# POST_BUILD
-# COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} ${unres_test_dest}
-# )
-#ENDFOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
#=========================================
-# Generate data test files
-#=========================================
-# test_single_ala.sh
+# TESTS
#=========================================
-#FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh
-#"#!/bin/sh
-#export POT=GB
-#export PREFIX=ala10
+# MESSAGE (STATUS "${MPI_Fortran_LIBRARIES}")
+ if ("${MPI_Fortran_LIBRARIES}" MATCHES "lam")
+ MESSAGE (STATUS "LAM MPI library detected")
+ set (boot_lam "-boot")
+ else()
+ set (boot_lam "")
+ endif()
+
+ if (UNRES_SRUN)
+ set (np "-n")
+ set (mpiexec "srun")
+ elseif(UNRES_MPIRUN)
+ set (np "-np")
+ set (mpiexec "mpirun")
+ else()
+ set (np "-np")
+ set (mpiexec "mpiexec")
+ endif()
+
+
+FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/scripts/cluster_wham_mpi_E0LL2Y.sh
+"#!/bin/sh
+export POT=GB
+export INPUT=$1
+export INTIN=1L2Y_wham
+export OUTPUT=1L2Y_clust
+export PDB=CART
+export COORD=CX
+export PRINTCOOR=PRINT_PDB
#-----------------------------------------------------------------------------
-#UNRES_BIN=./${UNRES_BIN}
+CLUSTER_WHAM_BIN=${CMAKE_BINARY_DIR}/bin/${UNRES_CLUSTER_WHAM_M_BIN}
#-----------------------------------------------------------------------------
-#DD=${CMAKE_SOURCE_DIR}/PARAM
-#export BONDPAR=$DD/bond.parm
-#export THETPAR=$DD/thetaml.5parm
-#export ROTPAR=$DD/scgauss.parm
-#export TORPAR=$DD/torsion_631Gdp.parm
-#export TORDPAR=$DD/torsion_double_631Gdp.parm
-#export ELEPAR=$DD/electr_631Gdp.parm
-#export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
-#export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
-#export SCPPAR=$DD/scp.parm
-#export SCCORPAR=$DD/rotcorr_AM1.parm
-#export PATTERN=$DD/patterns.cart
+DD=${CMAKE_SOURCE_DIR}/PARAM
+export BONDPAR=$DD/bond_AM1.parm
+export THETPAR=$DD/theta_abinitio.parm
+export ROTPAR=$DD/rotamers_AM1_aura.10022007.parm
+export TORPAR=$DD/torsion_631Gdp.parm
+export TORDPAR=$DD/torsion_double_631Gdp.parm
+export ELEPAR=$DD/electr_631Gdp.parm
+export SIDEPAR=$DD/scinter_$POT.parm
+export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
+export SCPPAR=$DD/scp.parm
+export SCCORPAR=$DD/sccor_am1_pawel.dat
+export THETPARPDB=$DD/thetaml.5parm
+export ROTPARPDB=$DD/scgauss.parm
+export PATTERN=$DD/patterns.cart
+export CONTFUNC=GB
+export SIDEP=$DD/contact.3.parm
+export SCRATCHDIR=.
#-----------------------------------------------------------------------------
-#$UNRES_BIN
-#")
+echo CTEST_FULL_OUTPUT
+${mpiexec} ${boot_lam} ${np} $2 $CLUSTER_WHAM_BIN
+./cluster_wham_check.sh $1
+")
-#=========================================
-# ala10.inp
-#=========================================
+#
+# File permissions workaround
+#
+FILE( COPY ${CMAKE_CURRENT_BINARY_DIR}/scripts/cluster_wham_mpi_E0LL2Y.sh
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
+ FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+)
-#file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/ala10.inp
-#"ala10 unblocked
-#SEED=-1111333 MD ONE_LETTER rescale_mode=2 PDBOUT
-#nstep=15000 ntwe=100 ntwx=1000 dt=0.1 lang=0 tbf t_bath=300 damax=1.0 &
-#reset_moment=1000 reset_vel=1000 MDPDB
-#WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
-#WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
-#WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
-#WVDWPP=0.11371 WHPB=1.00000 &
-#CUTOFF=7.00000 WCORR4=0.00000
-#12
-#XAAAAAAAAAAX
-# 0
-# 0
-# 90.0000 90.0000 90.0000 90.000 90.000 90.000 90.000 90.000
-# 90.0000 90.0000
-# 180.0000 180.0000 180.0000 180.000 180.000 180.000 180.000 180.000
-# 180.0000
-# 110.0000 110.0000 110.0000 100.000 110.000 100.000 110.000 110.000
-# 110.0000 110.0000
-# -120.0000 -120.0000 -120.000 -120.000 -120.000 -120.000 -120.000 -120.000
-# -120.0000 -120.0000
-#")
+FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/cluster_wham_check.sh
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
+ FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+)
+FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y_clust.inp
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
-# Add tests
+FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y_wham.cx
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
-#if(NOT UNRES_WITH_MPI)
+FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y.pdb
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
-# add_test(NAME UNRES_MD_Ala10 COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh )
-#endif(NOT UNRES_WITH_MPI)
+if(UNRES_MD_FF STREQUAL "E0LL2Y")
+# add_test(NAME CLUSTER_WHAM_M_remd COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/cluster_wham_mpi_E0LL2Y.sh 1L2Y_clust 2 )
+endif(UNRES_MD_FF STREQUAL "E0LL2Y")