From mauche at cygnus.llnl.gov Tue May 8 13:25:51 2007 From: mauche at cygnus.llnl.gov (Christopher W. Mauche) Date: Tue, 8 May 2007 11:25:51 -0700 (PDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov Message-ID: <200705081825.l48IPp1s019410@cygnus.llnl.gov> Dear fellow FLASHers, I just downloaded a new clean version of flash v2.5 to zeus.llnl.gov, and attempted to test/verify it by running the sedov test problem. I was able to unpack and compile the code, but find an error when I run it. Specifically: > ./setup sedov -auto > gmake > cd object > cp ../setups/sedov/flash.par flash.par > srun -N1 -n2 -p pdebug flash2 "get_parm_from_context: igeomx,igeomy,igeomz: 4599616371426034975 4621819117588971520 4591870180066957722" ERROR: invalid mesh geometry, check igeom{x,y,z} "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" [1] [MPI Abort by user] Aborting Program! srun: mvapich: May 08 11:18:01: ABORT from MPI rank 1 [on zeus13] srun: error: zeus13: task1: Exited with exit code 1 srun: error: zeus13: task0: Killed where the lines in quotes are from a print statement I added to FLASH2.5/source/mesh/amr/init_mesh.F90 [just below the line "call get_parm_from_context(GLOBAL_PARM_CONTEXT, "igeomz", igeomz)"], which is the source of the error. It appears that igeom{x,y,z} is read in properly by one of the processors, but not by the second one. If I restrict the run to one processor, I get a different error: > srun -N1 -n1 -p pdebug flash2 "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" flash: initializing for sedov problem. p_ambient = 1.00000000000000008E-5 rho_ambient= 1. gamma = 1.3999999999999999 exp_energy = 1. r_init = 1.3671875E-2 p_exp = 681.16756574500903 xctr = 0.5 yctr = 0.5 zctr = 0.5 ndim = 2 nsubzones = 7 0 - MPI_SSEND : Invalid rank 1 [0] [] Aborting Program! srun: mvapich: May 08 11:23:39: ABORT from MPI rank 0 [on zeus13] srun: error: zeus13: task0: Exited with exit code 70 Does anyone have an idea what might be causing these problems, and what I can do about them? Please note that Flash v2.5 _used_ to work for me on zeus, but now it fails with these errors. Thanks, Chris Mauche PS: For the record, my FLASH2.5/source/sites/zeus.llnl.gov/Makefile.h is: # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux # Created for zeus.llnl.gov by nathan and cal. # # Fedora Core 3 # Intel Linux Fortran 9.0 # hdf5-1.6.5 (icc90) # mpich-1.2.7 (icc90) #---------------------------------------------------------------------------- # Set the HDF/HDF5 library paths -- these need to be updated for your system #---------------------------------------------------------------------------- MPI_PATH = HDF4_PATH = HDF5_PATH = /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel ZLIB_PATH = PAPI_PATH = PAPI_FLAGS = NCMPI_PATH = MPE_PATH = #---------------------------------------------------------------------------- # Compiler and linker commands # # We use the f90 compiler as the linker, so some C libraries may explicitly # need to be added into the link line. #---------------------------------------------------------------------------- FCOMP = mpipathf90 CCOMP = mpipathcc CPPCOMP = mpipathCC LINK = mpipathf90 # pre-processor flag PP = -D #----------------------------------------------------------------------------- # Compilation flags # # Three sets of compilation/linking flags are defined: one for optimized code # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). # Passing these flags to the setup script will cause the value associated with # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to # be incorporated into the final Makefile. For example, passing "-opt" to the # setup script will cause the flags following "FFLAGS_OPT" to be assigned to # "FFLAGS" in the final Makefile. If none of these flags passed, the default # behavior will match that of the "-opt" flag. # In general, "-opt" is meant to optimize compilation and linking. "-debug" # should enable runtime bounds checking, debugger symbols, and other compiler- # specific debugging options. "-test" is useful for testing different # combinations of compiler flags particular to your individual system. #---------------------------------------------------------------------------- FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check output_conversion -warn all -real_size 64 FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE CFLAGS_HDF5 = -I $(HDF5_PATH)/include CFLAGS_NCMPI = -I $(NCMPI_PATH)/include CFLAGS_MPI = -I$(MPI_PATH)/include #---------------------------------------------------------------------------- # Linker flags # # There is a seperate version of the linker flags for each of the _OPT, # _DEBUG, and _TEST cases. #---------------------------------------------------------------------------- LFLAGS_OPT = -r8 -i8 -Ur -g -o LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o LFLAGS_TEST = -r8 -i4 -Vaxlib -o #---------------------------------------------------------------------------- # Library specific linking # # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to # create a macro in this Makefile.h for LIB_xxx, which will be added to the # link line when FLASH is built. This allows us to switch between different # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST # library macro to add any performance-minded libraries (like fast math), # depending on how FLASH was setup. #---------------------------------------------------------------------------- LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz LIB_PNG = -lpng LIB_MPI = LIB_NCMPI = LIB_MPE = #---------------------------------------------------------------------------- # Additional machine-dependent object files # # Add any machine specific files here -- they will be compiled and linked # when FLASH is built. #---------------------------------------------------------------------------- MACHOBJ = #---------------------------------------------------------------------------- # Additional commands #---------------------------------------------------------------------------- MV = mv -f AR = ar -r RM = rm -f CD = cd RL = ranlib ECHO = echo zeus287{mauche}445: cat Makefile.h # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux # Created for zeus.llnl.gov by nathan and cal. # # Fedora Core 3 # Intel Linux Fortran 9.0 # hdf5-1.6.5 (icc90) # mpich-1.2.7 (icc90) #---------------------------------------------------------------------------- # Set the HDF/HDF5 library paths -- these need to be updated for your system #---------------------------------------------------------------------------- MPI_PATH = HDF4_PATH = HDF5_PATH = /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel ZLIB_PATH = PAPI_PATH = PAPI_FLAGS = NCMPI_PATH = MPE_PATH = #---------------------------------------------------------------------------- # Compiler and linker commands # # We use the f90 compiler as the linker, so some C libraries may explicitly # need to be added into the link line. #---------------------------------------------------------------------------- FCOMP = mpipathf90 CCOMP = mpipathcc CPPCOMP = mpipathCC LINK = mpipathf90 # pre-processor flag PP = -D #----------------------------------------------------------------------------- # Compilation flags # # Three sets of compilation/linking flags are defined: one for optimized code # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). # Passing these flags to the setup script will cause the value associated with # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to # be incorporated into the final Makefile. For example, passing "-opt" to the # setup script will cause the flags following "FFLAGS_OPT" to be assigned to # "FFLAGS" in the final Makefile. If none of these flags passed, the default # behavior will match that of the "-opt" flag. # In general, "-opt" is meant to optimize compilation and linking. "-debug" # should enable runtime bounds checking, debugger symbols, and other compiler- # specific debugging options. "-test" is useful for testing different # combinations of compiler flags particular to your individual system. #---------------------------------------------------------------------------- FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check output_conversion -warn all -real_size 64 FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE CFLAGS_HDF5 = -I $(HDF5_PATH)/include CFLAGS_NCMPI = -I $(NCMPI_PATH)/include CFLAGS_MPI = -I$(MPI_PATH)/include #---------------------------------------------------------------------------- # Linker flags # # There is a seperate version of the linker flags for each of the _OPT, # _DEBUG, and _TEST cases. #---------------------------------------------------------------------------- LFLAGS_OPT = -r8 -i8 -Ur -g -o LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o LFLAGS_TEST = -r8 -i4 -Vaxlib -o #---------------------------------------------------------------------------- # Library specific linking # # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to # create a macro in this Makefile.h for LIB_xxx, which will be added to the # link line when FLASH is built. This allows us to switch between different # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST # library macro to add any performance-minded libraries (like fast math), # depending on how FLASH was setup. #---------------------------------------------------------------------------- LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz LIB_PNG = -lpng LIB_MPI = LIB_NCMPI = LIB_MPE = #---------------------------------------------------------------------------- # Additional machine-dependent object files # # Add any machine specific files here -- they will be compiled and linked # when FLASH is built. #---------------------------------------------------------------------------- MACHOBJ = #---------------------------------------------------------------------------- # Additional commands #---------------------------------------------------------------------------- MV = mv -f AR = ar -r RM = rm -f CD = cd RL = ranlib ECHO = echo From cyoung at grad.physics.sunysb.edu Tue May 8 15:15:46 2007 From: cyoung at grad.physics.sunysb.edu (Clint Young) Date: Tue, 8 May 2007 16:15:46 -0400 (EDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov In-Reply-To: <200705081825.l48IPp1s019410@cygnus.llnl.gov> Message-ID: On Tue, 8 May 2007, Christopher W. Mauche wrote: > Dear fellow FLASHers, > > I just downloaded a new clean version of flash v2.5 to zeus.llnl.gov, and > attempted to test/verify it by running the sedov test problem. I was able to > unpack and compile the code, but find an error when I run it. Specifically: > > > ./setup sedov -auto > > gmake > > cd object > > cp ../setups/sedov/flash.par flash.par > > srun -N1 -n2 -p pdebug flash2 > "get_parm_from_context: igeomx,igeomy,igeomz: 4599616371426034975 > 4621819117588971520 4591870180066957722" > ERROR: invalid mesh geometry, check igeom{x,y,z} > "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" > [1] [MPI Abort by user] Aborting Program! > srun: mvapich: May 08 11:18:01: ABORT from MPI rank 1 [on zeus13] > srun: error: zeus13: task1: Exited with exit code 1 > srun: error: zeus13: task0: Killed > > where the lines in quotes are from a print statement I added to > FLASH2.5/source/mesh/amr/init_mesh.F90 [just below the line > "call get_parm_from_context(GLOBAL_PARM_CONTEXT, "igeomz", igeomz)"], > which is the source of the error. It appears that igeom{x,y,z} is read in > properly by one of the processors, but not by the second one. > > If I restrict the run to one processor, I get a different error: > > > srun -N1 -n1 -p pdebug flash2 > "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" > flash: initializing for sedov problem. > p_ambient = 1.00000000000000008E-5 > rho_ambient= 1. > gamma = 1.3999999999999999 > exp_energy = 1. > r_init = 1.3671875E-2 > p_exp = 681.16756574500903 > xctr = 0.5 > yctr = 0.5 > zctr = 0.5 > ndim = 2 > nsubzones = 7 > 0 - MPI_SSEND : Invalid rank 1 > [0] [] Aborting Program! > srun: mvapich: May 08 11:23:39: ABORT from MPI rank 0 [on zeus13] > srun: error: zeus13: task0: Exited with exit code 70 > > Does anyone have an idea what might be causing these problems, and what I can do > about them? Please note that Flash v2.5 _used_ to work for me on zeus, but now > it fails with these errors. > > Thanks, > Chris Mauche > > PS: For the record, my FLASH2.5/source/sites/zeus.llnl.gov/Makefile.h is: > > # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux > # Created for zeus.llnl.gov by nathan and cal. > # > # Fedora Core 3 > # Intel Linux Fortran 9.0 > # hdf5-1.6.5 (icc90) > # mpich-1.2.7 (icc90) > > #---------------------------------------------------------------------------- > # Set the HDF/HDF5 library paths -- these need to be updated for your system > #---------------------------------------------------------------------------- > > MPI_PATH = > HDF4_PATH = > HDF5_PATH = > /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel > > ZLIB_PATH = > > PAPI_PATH = > PAPI_FLAGS = > > NCMPI_PATH = > MPE_PATH = > > #---------------------------------------------------------------------------- > # Compiler and linker commands > # > # We use the f90 compiler as the linker, so some C libraries may explicitly > # need to be added into the link line. > #---------------------------------------------------------------------------- > > FCOMP = mpipathf90 > CCOMP = mpipathcc > CPPCOMP = mpipathCC > LINK = mpipathf90 > > # pre-processor flag > > PP = -D > > #----------------------------------------------------------------------------- > # Compilation flags > # > # Three sets of compilation/linking flags are defined: one for optimized code > # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). > # Passing these flags to the setup script will cause the value associated with > # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to > # be incorporated into the final Makefile. For example, passing "-opt" to the > # setup script will cause the flags following "FFLAGS_OPT" to be assigned to > # "FFLAGS" in the final Makefile. If none of these flags passed, the default > # behavior will match that of the "-opt" flag. > # In general, "-opt" is meant to optimize compilation and linking. "-debug" > # should enable runtime bounds checking, debugger symbols, and other compiler- > # specific debugging options. "-test" is useful for testing different > # combinations of compiler flags particular to your individual system. > #---------------------------------------------------------------------------- > > FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g > FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check > output_conversion -warn all -real_size 64 > FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 > > > CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g > CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE > CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE > > CFLAGS_HDF5 = -I $(HDF5_PATH)/include > CFLAGS_NCMPI = -I $(NCMPI_PATH)/include > CFLAGS_MPI = -I$(MPI_PATH)/include > > #---------------------------------------------------------------------------- > # Linker flags > # > # There is a seperate version of the linker flags for each of the _OPT, > # _DEBUG, and _TEST cases. > #---------------------------------------------------------------------------- > > LFLAGS_OPT = -r8 -i8 -Ur -g -o > LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o > LFLAGS_TEST = -r8 -i4 -Vaxlib -o > > #---------------------------------------------------------------------------- > # Library specific linking > # > # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to > # create a macro in this Makefile.h for LIB_xxx, which will be added to the > # link line when FLASH is built. This allows us to switch between different > # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST > # library macro to add any performance-minded libraries (like fast math), > # depending on how FLASH was setup. > #---------------------------------------------------------------------------- > > LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg > LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz > LIB_PNG = -lpng > > LIB_MPI = > LIB_NCMPI = > LIB_MPE = > > > #---------------------------------------------------------------------------- > # Additional machine-dependent object files > # > # Add any machine specific files here -- they will be compiled and linked > # when FLASH is built. > #---------------------------------------------------------------------------- > > MACHOBJ = > > #---------------------------------------------------------------------------- > # Additional commands > #---------------------------------------------------------------------------- > > MV = mv -f > AR = ar -r > RM = rm -f > CD = cd > RL = ranlib > ECHO = echo > > zeus287{mauche}445: cat Makefile.h > # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux > # Created for zeus.llnl.gov by nathan and cal. > # > # Fedora Core 3 > # Intel Linux Fortran 9.0 > # hdf5-1.6.5 (icc90) > # mpich-1.2.7 (icc90) > > #---------------------------------------------------------------------------- > # Set the HDF/HDF5 library paths -- these need to be updated for your system > #---------------------------------------------------------------------------- > > MPI_PATH = > HDF4_PATH = > HDF5_PATH = > /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel > > ZLIB_PATH = > > PAPI_PATH = > PAPI_FLAGS = > > NCMPI_PATH = > MPE_PATH = > > #---------------------------------------------------------------------------- > # Compiler and linker commands > # > # We use the f90 compiler as the linker, so some C libraries may explicitly > # need to be added into the link line. > #---------------------------------------------------------------------------- > > FCOMP = mpipathf90 > CCOMP = mpipathcc > CPPCOMP = mpipathCC > LINK = mpipathf90 > > # pre-processor flag > > PP = -D > > #----------------------------------------------------------------------------- > # Compilation flags > # > # Three sets of compilation/linking flags are defined: one for optimized code > # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). > # Passing these flags to the setup script will cause the value associated with > # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to > # be incorporated into the final Makefile. For example, passing "-opt" to the > # setup script will cause the flags following "FFLAGS_OPT" to be assigned to > # "FFLAGS" in the final Makefile. If none of these flags passed, the default > # behavior will match that of the "-opt" flag. > # In general, "-opt" is meant to optimize compilation and linking. "-debug" > # should enable runtime bounds checking, debugger symbols, and other compiler- > # specific debugging options. "-test" is useful for testing different > # combinations of compiler flags particular to your individual system. > #---------------------------------------------------------------------------- > > FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g > FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check > output_conversion -warn all -real_size 64 > FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 > > > CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g > CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE > CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE > > CFLAGS_HDF5 = -I $(HDF5_PATH)/include > CFLAGS_NCMPI = -I $(NCMPI_PATH)/include > CFLAGS_MPI = -I$(MPI_PATH)/include > > #---------------------------------------------------------------------------- > # Linker flags > # > # There is a seperate version of the linker flags for each of the _OPT, > # _DEBUG, and _TEST cases. > #---------------------------------------------------------------------------- > > LFLAGS_OPT = -r8 -i8 -Ur -g -o > LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o > LFLAGS_TEST = -r8 -i4 -Vaxlib -o > > #---------------------------------------------------------------------------- > # Library specific linking > # > # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to > # create a macro in this Makefile.h for LIB_xxx, which will be added to the > # link line when FLASH is built. This allows us to switch between different > # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST > # library macro to add any performance-minded libraries (like fast math), > # depending on how FLASH was setup. > #---------------------------------------------------------------------------- > > LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg > LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz > LIB_PNG = -lpng > > LIB_MPI = > LIB_NCMPI = > LIB_MPE = > > > #---------------------------------------------------------------------------- > # Additional machine-dependent object files > # > # Add any machine specific files here -- they will be compiled and linked > # when FLASH is built. > #---------------------------------------------------------------------------- > > MACHOBJ = > > #---------------------------------------------------------------------------- > # Additional commands > #---------------------------------------------------------------------------- > > MV = mv -f > AR = ar -r > RM = rm -f > CD = cd > RL = ranlib > ECHO = echo > From mauche at cygnus.llnl.gov Thu May 10 16:25:46 2007 From: mauche at cygnus.llnl.gov (Christopher W. Mauche) Date: Thu, 10 May 2007 14:25:46 -0700 (PDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov Message-ID: <200705102125.l4ALPkk1009490@cygnus.llnl.gov> Dear fellow FLASHers, For the record, it appears that the problem that I was having with flash2.5 on zeus.llnl.gov was due to the use of -i8 in the Makefile. As suggested by Sheila Faulkner here at LLNL, I changed -i8 to -i4 everywhere in the Makefile and was then able to run the sedov test problem. According to Sheila, "-i8 on the compile line can cause troubles with the MPI library, which expects most of its integer input parameters (ranks, counts, etc) to be 4 byte integers." I don't know if this impacts other setups, and I don't know what other problems this change might cause, but so far things look good. Fingers crossed ... Chris Mauche From bernalcg at astroscu.unam.mx Wed May 23 15:18:02 2007 From: bernalcg at astroscu.unam.mx (Cristian Giovanny Bernal) Date: Wed, 23 May 2007 14:18:02 -0600 Subject: [FLASH-USERS] HDF5 or segmentation fault... Message-ID: <20070523194724.M92892@astroscu.unam.mx> Hello flash-user, I am trying to install FLASH2.5 in a new linux machine but I have very problems. The libraries that I am using are: 1. Fortran 9.1 (noncommercial version) 2. MPI 2 3. HDF5 1.6.5 But I obtain an error very similar to which David(2005) & Owen(2004) report in FLASH_WEB. How I solved this problem (in the sedov example)? error 1: ------------------ guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 object/flash2: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory ------------------ In order to solve this, I followed the suggestions (FAQs) of the manual (setenv LD_LIBRARY_PATH /usr/local/src/hdf5-1.6.5/hdf5/lib), but did not give results. Then I followed the suggestions that the users did to him to Owen (I add the follow line in the linking flags...LFLAGS_HDF5 = -Wl,-R/usr/local/src/hdf5-1.6.5/hdf5/lib)... but I obtained another message of error: eroor 2: ------------------------------ guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 read_parameters: unable to open parameter file "flash.par" abort_flash called. See log file for details. Calling MPI_Abort() for immediate shutdown! forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source flash2 0818F844 Unknown Unknown Unknown flash2 0818F837 Unknown Unknown Unknown Stack trace terminated abnormally. rank 0 in job 82 gaae1_44953 caused collective abort of all ranks exit status of rank 0: return code 174 ------------------------------- Does anyone have any ideas? Thank you very much, Giovanny -- Instituto de Astronomia Universid ad Nacional Autonoma de Mexico (UNAM) http://www.astroscu.unam.mx From dubey at flash.uchicago.edu Wed May 23 16:58:23 2007 From: dubey at flash.uchicago.edu (Anshu Dubey) Date: Wed, 23 May 2007 16:58:23 -0500 (CDT) Subject: [FLASH-USERS] HDF5 or segmentation fault... In-Reply-To: <20070523194724.M92892@astroscu.unam.mx> References: <20070523194724.M92892@astroscu.unam.mx> Message-ID: <6964.75.3.149.91.1179957503.squirrel@flash.uchicago.edu> Cristin, You should either try to run the code in the object directory, which has the flash.par file, or copy the file to the directory that you are running from. It is an input file, and FLASH looks for it in the run directory. Anshu > Hello flash-user, > > I am trying to install FLASH2.5 in a new linux machine but I have very > problems. The libraries that I am using are: > > 1. Fortran 9.1 (noncommercial version) > 2. MPI 2 > 3. HDF5 1.6.5 > > But I obtain an error very similar to which David(2005) & Owen(2004) > report in > FLASH_WEB. > How I solved this problem (in the sedov example)? > > error 1: > ------------------ > guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 > object/flash2: error while loading shared libraries: libhdf5.so.0: cannot > open > shared object file: No such file or directory > ------------------ > > In order to solve this, I followed the suggestions (FAQs) of the manual > (setenv LD_LIBRARY_PATH /usr/local/src/hdf5-1.6.5/hdf5/lib), but did not > give > results. Then I followed the suggestions that the users did to him to Owen > (I > add the follow line in the linking flags...LFLAGS_HDF5 = > -Wl,-R/usr/local/src/hdf5-1.6.5/hdf5/lib)... but I obtained another > message of > error: > > eroor 2: > ------------------------------ > guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 > read_parameters: unable to open parameter file "flash.par" > > abort_flash called. See log file for details. > Calling MPI_Abort() for immediate shutdown! > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > flash2 0818F844 Unknown Unknown Unknown > flash2 0818F837 Unknown Unknown Unknown > > Stack trace terminated abnormally. > rank 0 in job 82 gaae1_44953 caused collective abort of all ranks > exit status of rank 0: return code 174 > ------------------------------- > > Does anyone have any ideas? > > Thank you very much, > Giovanny > > -- > Instituto de Astronomia > Universid > ad Nacional Autonoma de Mexico (UNAM) > http://www.astroscu.unam.mx > From dubey at flash.uchicago.edu Thu May 24 09:04:33 2007 From: dubey at flash.uchicago.edu (Anshu Dubey) Date: Thu, 24 May 2007 09:04:33 -0500 (CDT) Subject: [FLASH-USERS] Scientific Programmer's job at the Flash Center Message-ID: <49987.75.3.149.91.1180015473.squirrel@flash.uchicago.edu> Dear Flash-users The Code Group at the Flash Center has an opening for a Scientific Programmer. The Code Group is responsible for design, development and maintainance of the FLASH Code. The job description can be found at http://jobs.uchicago.edu, the requisition number for the position is 075988. We'd like to talk to you if you, or someone you know, is interested. Also, please feel free to forward this information to those who may not be on the list. Best, Anshu Dubey Code Group Leader phone : 773.834.2999 From ipatov at dtm.ciw.edu Fri May 25 17:53:28 2007 From: ipatov at dtm.ciw.edu (ipatov at dtm.ciw.edu) Date: Fri, 25 May 2007 18:53:28 -0400 (EDT) Subject: [FLASH-USERS] xflash for 3d; mass scalars Message-ID: <34452.10.101.1.203.1180133608.squirrel@www.dtm.ciw.edu> Dear Flash-users I was not able to make plots with xflash (I used FLASH2.5) for ms (mass scalars) for 3d model. For 2d runs everything works OK, but for 3d (for the same init-block) xflash does not want to make any plots for ms (ms_i are seen in the menue both for 'chk' and 'plt' files, but after pressing 'plot' I get only 'done reading'). It is also strange that for 3d I can make plots of density only for 'plt' files (but not for main 'chk' files for which I can make only histograms of density). For 'pressure' plots are making only for 'chk' files, not 'plt' files (for which only histograms of pressure are making). Again, everything is Ok for 2d. Best regards Sergei From mauche at cygnus.llnl.gov Tue May 8 13:25:51 2007 From: mauche at cygnus.llnl.gov (Christopher W. Mauche) Date: Tue, 8 May 2007 11:25:51 -0700 (PDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov Message-ID: <200705081825.l48IPp1s019410@cygnus.llnl.gov> Dear fellow FLASHers, I just downloaded a new clean version of flash v2.5 to zeus.llnl.gov, and attempted to test/verify it by running the sedov test problem. I was able to unpack and compile the code, but find an error when I run it. Specifically: > ./setup sedov -auto > gmake > cd object > cp ../setups/sedov/flash.par flash.par > srun -N1 -n2 -p pdebug flash2 "get_parm_from_context: igeomx,igeomy,igeomz: 4599616371426034975 4621819117588971520 4591870180066957722" ERROR: invalid mesh geometry, check igeom{x,y,z} "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" [1] [MPI Abort by user] Aborting Program! srun: mvapich: May 08 11:18:01: ABORT from MPI rank 1 [on zeus13] srun: error: zeus13: task1: Exited with exit code 1 srun: error: zeus13: task0: Killed where the lines in quotes are from a print statement I added to FLASH2.5/source/mesh/amr/init_mesh.F90 [just below the line "call get_parm_from_context(GLOBAL_PARM_CONTEXT, "igeomz", igeomz)"], which is the source of the error. It appears that igeom{x,y,z} is read in properly by one of the processors, but not by the second one. If I restrict the run to one processor, I get a different error: > srun -N1 -n1 -p pdebug flash2 "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" flash: initializing for sedov problem. p_ambient = 1.00000000000000008E-5 rho_ambient= 1. gamma = 1.3999999999999999 exp_energy = 1. r_init = 1.3671875E-2 p_exp = 681.16756574500903 xctr = 0.5 yctr = 0.5 zctr = 0.5 ndim = 2 nsubzones = 7 0 - MPI_SSEND : Invalid rank 1 [0] [] Aborting Program! srun: mvapich: May 08 11:23:39: ABORT from MPI rank 0 [on zeus13] srun: error: zeus13: task0: Exited with exit code 70 Does anyone have an idea what might be causing these problems, and what I can do about them? Please note that Flash v2.5 _used_ to work for me on zeus, but now it fails with these errors. Thanks, Chris Mauche PS: For the record, my FLASH2.5/source/sites/zeus.llnl.gov/Makefile.h is: # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux # Created for zeus.llnl.gov by nathan and cal. # # Fedora Core 3 # Intel Linux Fortran 9.0 # hdf5-1.6.5 (icc90) # mpich-1.2.7 (icc90) #---------------------------------------------------------------------------- # Set the HDF/HDF5 library paths -- these need to be updated for your system #---------------------------------------------------------------------------- MPI_PATH = HDF4_PATH = HDF5_PATH = /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel ZLIB_PATH = PAPI_PATH = PAPI_FLAGS = NCMPI_PATH = MPE_PATH = #---------------------------------------------------------------------------- # Compiler and linker commands # # We use the f90 compiler as the linker, so some C libraries may explicitly # need to be added into the link line. #---------------------------------------------------------------------------- FCOMP = mpipathf90 CCOMP = mpipathcc CPPCOMP = mpipathCC LINK = mpipathf90 # pre-processor flag PP = -D #----------------------------------------------------------------------------- # Compilation flags # # Three sets of compilation/linking flags are defined: one for optimized code # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). # Passing these flags to the setup script will cause the value associated with # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to # be incorporated into the final Makefile. For example, passing "-opt" to the # setup script will cause the flags following "FFLAGS_OPT" to be assigned to # "FFLAGS" in the final Makefile. If none of these flags passed, the default # behavior will match that of the "-opt" flag. # In general, "-opt" is meant to optimize compilation and linking. "-debug" # should enable runtime bounds checking, debugger symbols, and other compiler- # specific debugging options. "-test" is useful for testing different # combinations of compiler flags particular to your individual system. #---------------------------------------------------------------------------- FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check output_conversion -warn all -real_size 64 FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE CFLAGS_HDF5 = -I $(HDF5_PATH)/include CFLAGS_NCMPI = -I $(NCMPI_PATH)/include CFLAGS_MPI = -I$(MPI_PATH)/include #---------------------------------------------------------------------------- # Linker flags # # There is a seperate version of the linker flags for each of the _OPT, # _DEBUG, and _TEST cases. #---------------------------------------------------------------------------- LFLAGS_OPT = -r8 -i8 -Ur -g -o LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o LFLAGS_TEST = -r8 -i4 -Vaxlib -o #---------------------------------------------------------------------------- # Library specific linking # # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to # create a macro in this Makefile.h for LIB_xxx, which will be added to the # link line when FLASH is built. This allows us to switch between different # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST # library macro to add any performance-minded libraries (like fast math), # depending on how FLASH was setup. #---------------------------------------------------------------------------- LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz LIB_PNG = -lpng LIB_MPI = LIB_NCMPI = LIB_MPE = #---------------------------------------------------------------------------- # Additional machine-dependent object files # # Add any machine specific files here -- they will be compiled and linked # when FLASH is built. #---------------------------------------------------------------------------- MACHOBJ = #---------------------------------------------------------------------------- # Additional commands #---------------------------------------------------------------------------- MV = mv -f AR = ar -r RM = rm -f CD = cd RL = ranlib ECHO = echo zeus287{mauche}445: cat Makefile.h # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux # Created for zeus.llnl.gov by nathan and cal. # # Fedora Core 3 # Intel Linux Fortran 9.0 # hdf5-1.6.5 (icc90) # mpich-1.2.7 (icc90) #---------------------------------------------------------------------------- # Set the HDF/HDF5 library paths -- these need to be updated for your system #---------------------------------------------------------------------------- MPI_PATH = HDF4_PATH = HDF5_PATH = /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel ZLIB_PATH = PAPI_PATH = PAPI_FLAGS = NCMPI_PATH = MPE_PATH = #---------------------------------------------------------------------------- # Compiler and linker commands # # We use the f90 compiler as the linker, so some C libraries may explicitly # need to be added into the link line. #---------------------------------------------------------------------------- FCOMP = mpipathf90 CCOMP = mpipathcc CPPCOMP = mpipathCC LINK = mpipathf90 # pre-processor flag PP = -D #----------------------------------------------------------------------------- # Compilation flags # # Three sets of compilation/linking flags are defined: one for optimized code # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). # Passing these flags to the setup script will cause the value associated with # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to # be incorporated into the final Makefile. For example, passing "-opt" to the # setup script will cause the flags following "FFLAGS_OPT" to be assigned to # "FFLAGS" in the final Makefile. If none of these flags passed, the default # behavior will match that of the "-opt" flag. # In general, "-opt" is meant to optimize compilation and linking. "-debug" # should enable runtime bounds checking, debugger symbols, and other compiler- # specific debugging options. "-test" is useful for testing different # combinations of compiler flags particular to your individual system. #---------------------------------------------------------------------------- FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check output_conversion -warn all -real_size 64 FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE CFLAGS_HDF5 = -I $(HDF5_PATH)/include CFLAGS_NCMPI = -I $(NCMPI_PATH)/include CFLAGS_MPI = -I$(MPI_PATH)/include #---------------------------------------------------------------------------- # Linker flags # # There is a seperate version of the linker flags for each of the _OPT, # _DEBUG, and _TEST cases. #---------------------------------------------------------------------------- LFLAGS_OPT = -r8 -i8 -Ur -g -o LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o LFLAGS_TEST = -r8 -i4 -Vaxlib -o #---------------------------------------------------------------------------- # Library specific linking # # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to # create a macro in this Makefile.h for LIB_xxx, which will be added to the # link line when FLASH is built. This allows us to switch between different # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST # library macro to add any performance-minded libraries (like fast math), # depending on how FLASH was setup. #---------------------------------------------------------------------------- LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz LIB_PNG = -lpng LIB_MPI = LIB_NCMPI = LIB_MPE = #---------------------------------------------------------------------------- # Additional machine-dependent object files # # Add any machine specific files here -- they will be compiled and linked # when FLASH is built. #---------------------------------------------------------------------------- MACHOBJ = #---------------------------------------------------------------------------- # Additional commands #---------------------------------------------------------------------------- MV = mv -f AR = ar -r RM = rm -f CD = cd RL = ranlib ECHO = echo From cyoung at grad.physics.sunysb.edu Tue May 8 15:15:46 2007 From: cyoung at grad.physics.sunysb.edu (Clint Young) Date: Tue, 8 May 2007 16:15:46 -0400 (EDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov In-Reply-To: <200705081825.l48IPp1s019410@cygnus.llnl.gov> Message-ID: On Tue, 8 May 2007, Christopher W. Mauche wrote: > Dear fellow FLASHers, > > I just downloaded a new clean version of flash v2.5 to zeus.llnl.gov, and > attempted to test/verify it by running the sedov test problem. I was able to > unpack and compile the code, but find an error when I run it. Specifically: > > > ./setup sedov -auto > > gmake > > cd object > > cp ../setups/sedov/flash.par flash.par > > srun -N1 -n2 -p pdebug flash2 > "get_parm_from_context: igeomx,igeomy,igeomz: 4599616371426034975 > 4621819117588971520 4591870180066957722" > ERROR: invalid mesh geometry, check igeom{x,y,z} > "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" > [1] [MPI Abort by user] Aborting Program! > srun: mvapich: May 08 11:18:01: ABORT from MPI rank 1 [on zeus13] > srun: error: zeus13: task1: Exited with exit code 1 > srun: error: zeus13: task0: Killed > > where the lines in quotes are from a print statement I added to > FLASH2.5/source/mesh/amr/init_mesh.F90 [just below the line > "call get_parm_from_context(GLOBAL_PARM_CONTEXT, "igeomz", igeomz)"], > which is the source of the error. It appears that igeom{x,y,z} is read in > properly by one of the processors, but not by the second one. > > If I restrict the run to one processor, I get a different error: > > > srun -N1 -n1 -p pdebug flash2 > "get_parm_from_context: igeomx,igeomy,igeomz: -1 -1 -1" > flash: initializing for sedov problem. > p_ambient = 1.00000000000000008E-5 > rho_ambient= 1. > gamma = 1.3999999999999999 > exp_energy = 1. > r_init = 1.3671875E-2 > p_exp = 681.16756574500903 > xctr = 0.5 > yctr = 0.5 > zctr = 0.5 > ndim = 2 > nsubzones = 7 > 0 - MPI_SSEND : Invalid rank 1 > [0] [] Aborting Program! > srun: mvapich: May 08 11:23:39: ABORT from MPI rank 0 [on zeus13] > srun: error: zeus13: task0: Exited with exit code 70 > > Does anyone have an idea what might be causing these problems, and what I can do > about them? Please note that Flash v2.5 _used_ to work for me on zeus, but now > it fails with these errors. > > Thanks, > Chris Mauche > > PS: For the record, my FLASH2.5/source/sites/zeus.llnl.gov/Makefile.h is: > > # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux > # Created for zeus.llnl.gov by nathan and cal. > # > # Fedora Core 3 > # Intel Linux Fortran 9.0 > # hdf5-1.6.5 (icc90) > # mpich-1.2.7 (icc90) > > #---------------------------------------------------------------------------- > # Set the HDF/HDF5 library paths -- these need to be updated for your system > #---------------------------------------------------------------------------- > > MPI_PATH = > HDF4_PATH = > HDF5_PATH = > /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel > > ZLIB_PATH = > > PAPI_PATH = > PAPI_FLAGS = > > NCMPI_PATH = > MPE_PATH = > > #---------------------------------------------------------------------------- > # Compiler and linker commands > # > # We use the f90 compiler as the linker, so some C libraries may explicitly > # need to be added into the link line. > #---------------------------------------------------------------------------- > > FCOMP = mpipathf90 > CCOMP = mpipathcc > CPPCOMP = mpipathCC > LINK = mpipathf90 > > # pre-processor flag > > PP = -D > > #----------------------------------------------------------------------------- > # Compilation flags > # > # Three sets of compilation/linking flags are defined: one for optimized code > # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). > # Passing these flags to the setup script will cause the value associated with > # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to > # be incorporated into the final Makefile. For example, passing "-opt" to the > # setup script will cause the flags following "FFLAGS_OPT" to be assigned to > # "FFLAGS" in the final Makefile. If none of these flags passed, the default > # behavior will match that of the "-opt" flag. > # In general, "-opt" is meant to optimize compilation and linking. "-debug" > # should enable runtime bounds checking, debugger symbols, and other compiler- > # specific debugging options. "-test" is useful for testing different > # combinations of compiler flags particular to your individual system. > #---------------------------------------------------------------------------- > > FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g > FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check > output_conversion -warn all -real_size 64 > FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 > > > CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g > CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE > CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE > > CFLAGS_HDF5 = -I $(HDF5_PATH)/include > CFLAGS_NCMPI = -I $(NCMPI_PATH)/include > CFLAGS_MPI = -I$(MPI_PATH)/include > > #---------------------------------------------------------------------------- > # Linker flags > # > # There is a seperate version of the linker flags for each of the _OPT, > # _DEBUG, and _TEST cases. > #---------------------------------------------------------------------------- > > LFLAGS_OPT = -r8 -i8 -Ur -g -o > LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o > LFLAGS_TEST = -r8 -i4 -Vaxlib -o > > #---------------------------------------------------------------------------- > # Library specific linking > # > # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to > # create a macro in this Makefile.h for LIB_xxx, which will be added to the > # link line when FLASH is built. This allows us to switch between different > # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST > # library macro to add any performance-minded libraries (like fast math), > # depending on how FLASH was setup. > #---------------------------------------------------------------------------- > > LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg > LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz > LIB_PNG = -lpng > > LIB_MPI = > LIB_NCMPI = > LIB_MPE = > > > #---------------------------------------------------------------------------- > # Additional machine-dependent object files > # > # Add any machine specific files here -- they will be compiled and linked > # when FLASH is built. > #---------------------------------------------------------------------------- > > MACHOBJ = > > #---------------------------------------------------------------------------- > # Additional commands > #---------------------------------------------------------------------------- > > MV = mv -f > AR = ar -r > RM = rm -f > CD = cd > RL = ranlib > ECHO = echo > > zeus287{mauche}445: cat Makefile.h > # FLASH makefile definitions for the 64 bit Intel icc/ifort compiler on Linux > # Created for zeus.llnl.gov by nathan and cal. > # > # Fedora Core 3 > # Intel Linux Fortran 9.0 > # hdf5-1.6.5 (icc90) > # mpich-1.2.7 (icc90) > > #---------------------------------------------------------------------------- > # Set the HDF/HDF5 library paths -- these need to be updated for your system > #---------------------------------------------------------------------------- > > MPI_PATH = > HDF4_PATH = > HDF5_PATH = > /usr/global/tools/hdf5/installs/chaos_3_x86_64_ib/hdf5-1.6.5/parallel > > ZLIB_PATH = > > PAPI_PATH = > PAPI_FLAGS = > > NCMPI_PATH = > MPE_PATH = > > #---------------------------------------------------------------------------- > # Compiler and linker commands > # > # We use the f90 compiler as the linker, so some C libraries may explicitly > # need to be added into the link line. > #---------------------------------------------------------------------------- > > FCOMP = mpipathf90 > CCOMP = mpipathcc > CPPCOMP = mpipathCC > LINK = mpipathf90 > > # pre-processor flag > > PP = -D > > #----------------------------------------------------------------------------- > # Compilation flags > # > # Three sets of compilation/linking flags are defined: one for optimized code > # code ("-opt"), one for debugging ("-debug"), and one for testing ("-test"). > # Passing these flags to the setup script will cause the value associated with > # the corresponding keys (i.e. those ending in "_OPT", "_DEBUG", or "_TEST") to > # be incorporated into the final Makefile. For example, passing "-opt" to the > # setup script will cause the flags following "FFLAGS_OPT" to be assigned to > # "FFLAGS" in the final Makefile. If none of these flags passed, the default > # behavior will match that of the "-opt" flag. > # In general, "-opt" is meant to optimize compilation and linking. "-debug" > # should enable runtime bounds checking, debugger symbols, and other compiler- > # specific debugging options. "-test" is useful for testing different > # combinations of compiler flags particular to your individual system. > #---------------------------------------------------------------------------- > > FFLAGS_OPT = -c -r8 -i8 -m64 -march=opteron -O3 -g > FFLAGS_DEBUG = -c -g -r8 -i4 -check bounds -check format -check > output_conversion -warn all -real_size 64 > FFLAGS_TEST = -c -r8 -i4 -O2 -real_size 64 > > > CFLAGS_OPT = -c -O3 -r8 -i8 -m64 -march=opteron -g > CFLAGS_DEBUG = -c -g -debug extended -D_LARGEFILE64_SOURCE > CFLAGS_TEST = -c -O2 -D_LARGEFILE64_SOURCE > > CFLAGS_HDF5 = -I $(HDF5_PATH)/include > CFLAGS_NCMPI = -I $(NCMPI_PATH)/include > CFLAGS_MPI = -I$(MPI_PATH)/include > > #---------------------------------------------------------------------------- > # Linker flags > # > # There is a seperate version of the linker flags for each of the _OPT, > # _DEBUG, and _TEST cases. > #---------------------------------------------------------------------------- > > LFLAGS_OPT = -r8 -i8 -Ur -g -o > LFLAGS_DEBUG = -r8 -i4 -Vaxlib -g -o > LFLAGS_TEST = -r8 -i4 -Vaxlib -o > > #---------------------------------------------------------------------------- > # Library specific linking > # > # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to > # create a macro in this Makefile.h for LIB_xxx, which will be added to the > # link line when FLASH is built. This allows us to switch between different > # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST > # library macro to add any performance-minded libraries (like fast math), > # depending on how FLASH was setup. > #---------------------------------------------------------------------------- > > LIB_HDF4 = -L $(HDF4_PATH)/lib -lmfhdf -ldf -lz -ljpeg > LIB_HDF5 = $(HDF5_PATH)/lib/libhdf5.a -lz > LIB_PNG = -lpng > > LIB_MPI = > LIB_NCMPI = > LIB_MPE = > > > #---------------------------------------------------------------------------- > # Additional machine-dependent object files > # > # Add any machine specific files here -- they will be compiled and linked > # when FLASH is built. > #---------------------------------------------------------------------------- > > MACHOBJ = > > #---------------------------------------------------------------------------- > # Additional commands > #---------------------------------------------------------------------------- > > MV = mv -f > AR = ar -r > RM = rm -f > CD = cd > RL = ranlib > ECHO = echo > From mauche at cygnus.llnl.gov Thu May 10 16:25:46 2007 From: mauche at cygnus.llnl.gov (Christopher W. Mauche) Date: Thu, 10 May 2007 14:25:46 -0700 (PDT) Subject: [FLASH-USERS] problem with FLASH2.5/source/mesh/amr/init_mesh.F90 on zeus.llnl.gov Message-ID: <200705102125.l4ALPkk1009490@cygnus.llnl.gov> Dear fellow FLASHers, For the record, it appears that the problem that I was having with flash2.5 on zeus.llnl.gov was due to the use of -i8 in the Makefile. As suggested by Sheila Faulkner here at LLNL, I changed -i8 to -i4 everywhere in the Makefile and was then able to run the sedov test problem. According to Sheila, "-i8 on the compile line can cause troubles with the MPI library, which expects most of its integer input parameters (ranks, counts, etc) to be 4 byte integers." I don't know if this impacts other setups, and I don't know what other problems this change might cause, but so far things look good. Fingers crossed ... Chris Mauche From bernalcg at astroscu.unam.mx Wed May 23 15:18:02 2007 From: bernalcg at astroscu.unam.mx (Cristian Giovanny Bernal) Date: Wed, 23 May 2007 14:18:02 -0600 Subject: [FLASH-USERS] HDF5 or segmentation fault... Message-ID: <20070523194724.M92892@astroscu.unam.mx> Hello flash-user, I am trying to install FLASH2.5 in a new linux machine but I have very problems. The libraries that I am using are: 1. Fortran 9.1 (noncommercial version) 2. MPI 2 3. HDF5 1.6.5 But I obtain an error very similar to which David(2005) & Owen(2004) report in FLASH_WEB. How I solved this problem (in the sedov example)? error 1: ------------------ guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 object/flash2: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory ------------------ In order to solve this, I followed the suggestions (FAQs) of the manual (setenv LD_LIBRARY_PATH /usr/local/src/hdf5-1.6.5/hdf5/lib), but did not give results. Then I followed the suggestions that the users did to him to Owen (I add the follow line in the linking flags...LFLAGS_HDF5 = -Wl,-R/usr/local/src/hdf5-1.6.5/hdf5/lib)... but I obtained another message of error: eroor 2: ------------------------------ guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 read_parameters: unable to open parameter file "flash.par" abort_flash called. See log file for details. Calling MPI_Abort() for immediate shutdown! forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source flash2 0818F844 Unknown Unknown Unknown flash2 0818F837 Unknown Unknown Unknown Stack trace terminated abnormally. rank 0 in job 82 gaae1_44953 caused collective abort of all ranks exit status of rank 0: return code 174 ------------------------------- Does anyone have any ideas? Thank you very much, Giovanny -- Instituto de Astronomia Universid ad Nacional Autonoma de Mexico (UNAM) http://www.astroscu.unam.mx From dubey at flash.uchicago.edu Wed May 23 16:58:23 2007 From: dubey at flash.uchicago.edu (Anshu Dubey) Date: Wed, 23 May 2007 16:58:23 -0500 (CDT) Subject: [FLASH-USERS] HDF5 or segmentation fault... In-Reply-To: <20070523194724.M92892@astroscu.unam.mx> References: <20070523194724.M92892@astroscu.unam.mx> Message-ID: <6964.75.3.149.91.1179957503.squirrel@flash.uchicago.edu> Cristin, You should either try to run the code in the object directory, which has the flash.par file, or copy the file to the directory that you are running from. It is an input file, and FLASH looks for it in the run directory. Anshu > Hello flash-user, > > I am trying to install FLASH2.5 in a new linux machine but I have very > problems. The libraries that I am using are: > > 1. Fortran 9.1 (noncommercial version) > 2. MPI 2 > 3. HDF5 1.6.5 > > But I obtain an error very similar to which David(2005) & Owen(2004) > report in > FLASH_WEB. > How I solved this problem (in the sedov example)? > > error 1: > ------------------ > guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 > object/flash2: error while loading shared libraries: libhdf5.so.0: cannot > open > shared object file: No such file or directory > ------------------ > > In order to solve this, I followed the suggestions (FAQs) of the manual > (setenv LD_LIBRARY_PATH /usr/local/src/hdf5-1.6.5/hdf5/lib), but did not > give > results. Then I followed the suggestions that the users did to him to Owen > (I > add the follow line in the linking flags...LFLAGS_HDF5 = > -Wl,-R/usr/local/src/hdf5-1.6.5/hdf5/lib)... but I obtained another > message of > error: > > eroor 2: > ------------------------------ > guest at gaae1:~/FLASH2.5$ mpirun -np 1 object/flash2 > read_parameters: unable to open parameter file "flash.par" > > abort_flash called. See log file for details. > Calling MPI_Abort() for immediate shutdown! > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > flash2 0818F844 Unknown Unknown Unknown > flash2 0818F837 Unknown Unknown Unknown > > Stack trace terminated abnormally. > rank 0 in job 82 gaae1_44953 caused collective abort of all ranks > exit status of rank 0: return code 174 > ------------------------------- > > Does anyone have any ideas? > > Thank you very much, > Giovanny > > -- > Instituto de Astronomia > Universid > ad Nacional Autonoma de Mexico (UNAM) > http://www.astroscu.unam.mx > From dubey at flash.uchicago.edu Thu May 24 09:04:33 2007 From: dubey at flash.uchicago.edu (Anshu Dubey) Date: Thu, 24 May 2007 09:04:33 -0500 (CDT) Subject: [FLASH-USERS] Scientific Programmer's job at the Flash Center Message-ID: <49987.75.3.149.91.1180015473.squirrel@flash.uchicago.edu> Dear Flash-users The Code Group at the Flash Center has an opening for a Scientific Programmer. The Code Group is responsible for design, development and maintainance of the FLASH Code. The job description can be found at http://jobs.uchicago.edu, the requisition number for the position is 075988. We'd like to talk to you if you, or someone you know, is interested. Also, please feel free to forward this information to those who may not be on the list. Best, Anshu Dubey Code Group Leader phone : 773.834.2999 From ipatov at dtm.ciw.edu Fri May 25 17:53:28 2007 From: ipatov at dtm.ciw.edu (ipatov at dtm.ciw.edu) Date: Fri, 25 May 2007 18:53:28 -0400 (EDT) Subject: [FLASH-USERS] xflash for 3d; mass scalars Message-ID: <34452.10.101.1.203.1180133608.squirrel@www.dtm.ciw.edu> Dear Flash-users I was not able to make plots with xflash (I used FLASH2.5) for ms (mass scalars) for 3d model. For 2d runs everything works OK, but for 3d (for the same init-block) xflash does not want to make any plots for ms (ms_i are seen in the menue both for 'chk' and 'plt' files, but after pressing 'plot' I get only 'done reading'). It is also strange that for 3d I can make plots of density only for 'plt' files (but not for main 'chk' files for which I can make only histograms of density). For 'pressure' plots are making only for 'chk' files, not 'plt' files (for which only histograms of pressure are making). Again, everything is Ok for 2d. Best regards Sergei