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HiFiLES / HiFiLES-solver

High Fidelity Large Eddy Simulation Solver
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compilation error #8

Closed amihaisilver closed 8 years ago

amihaisilver commented 10 years ago

Dear support,

I try to install the HiFiLES on a RedHat cluster with mpich, but the installation failed with the error below.

the system is : Red Hat Enterprise Linux Server release 6.4 (Santiago) Linux tamnun 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64

Attached are the installation logs. I appreciate your help.

make[1]: Entering directory `/usr/local/HiFiLES-solver-master/obj' CXX ../src/___bin_HiFiLES-global.o g++: 1.0.0": No such file or directory

: warning: missing terminating " character make[1]: *** [../src/___bin_HiFiLES-global.o] Error 1 make[1]: Leaving directory`/usr/local/HiFiLES-solver-master/obj' make: **\* [all-recursive] Error 1 The full installation log is below Thanks, Amihai cat configure_run.sh ###### # \file configure_run.sh # \brief Configuration script for HiFiLES # \author - Original code: SD++ developed by Patrice Castonguay, Antony Jameson, # Peter Vincent, David Williams (alphabetical by surname). # \- Current development: Aerospace Computing Laboratory (ACL) # Aero/Astro Department. Stanford University. # \version 0.1.0 # # High Fidelity Large Eddy Simulation (HiFiLES) Code. # Copyright (C) 2014 Aerospace Computing Laboratory (ACL). # # HiFiLES is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # HiFiLES is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with HiFiLES. If not, see http://www.gnu.org/licenses/. ###### # Standard (Helpful) Settings [Should not need to change these] export HIFILES_HOME=$(pwd) # --------------------------------------------------------------- # Basic User-Modifiable Build Settings [Change these as desired] NODE="CPU" # CPU or GPU CODE="RELEASE" # DEBUG or RELEASE BLAS="ATLAS" # ATLAS, STANDARD, ACCLERATE, or NO PARALLEL="YES" # YES or NO TECIO="NO" # YES or NO METIS="YES" # Build & link to the HiFiLES-supplied ParMETIS libraries? YES or NO # --------------------------------------------------------------- # Compiler Selections [Change compilers or add full filepaths if needed] CXX="g++" # C++ compiler - Typically g++ (default, GNU) or icpc (Intel) NVCC="nvcc" # NVidia CUDA compiler MPICC="mpicxx" # MPI C compiler # --------------------------------------------------------------- # Library & Header File Locations [Change filepaths as needed] BLAS_LIB="/usr/lib64/atlas" BLAS_INCLUDE="/usr/include/atlas-x86_64-base" TECIO_LIB="lib/tecio-2008/lib" TECIO_INCLUDE="lib/tecio-2008/include" CUDA_LIB="/usr/local/cuda/lib64" CUDA_INCLUDE="/usr/local/cuda/include" # If building the supplied ParMETIS libraries, need the MPI header location MPI_INCLUDE="/usr/include/mpich2-x86_64" # location of mpi.h # MPI_INCLUDE="/usr/include/openmpi-x86_64" # location of mpi.h # If NOT building the supplied ParMetis library, location of installed libraries PARMETIS_LIB="/usr/local/lib" # location of libparmetis.a PARMETIS_INCLUDE="/usr/local/include" # location of parmetis.h METIS_LIB="/usr/local/lib" # location of libmetis.a METIS_INCLUDE="/usr/local/include" # location of metis.h # --------------------------------------------------------------- # Run configure using the chosen options [Should not change this] if [[ "$NODE" == "GPU" ]] then _GPU=$NVCC else _GPU="NO" fi if [[ "$PARALLEL" == "YES" ]] then _MPI=$MPICC else _MPI="NO" PARMETIS_LIB="NO" PARMETIS_INCLUDE="NO" fi if [[ "$TECIO" == "NO" ]] then TECIO_LIB="NO" TECIO_INCLUDE="NO" fi ./configure --prefix=$HIFILES_RUN/.. \ --with-CXX=$CXX \ --with-BLAS=$BLAS \ --with-BLAS-lib=$BLAS_LIB \ --with-BLAS-include=$BLAS_INCLUDE \ --with-MPI=$_MPI \ --with-MPI-include=$MPI_INCLUDE \ --with-CUDA=$_GPU \ --with-CUDA-lib=$CUDA_LIB \ --with-CUDA-include=$CUDA_INCLUDE \ --with-ParMetis-lib=$PARMETIS_LIB \ --with-ParMetis-include=$PARMETIS_INCLUDE \ --with-Metis-lib=$METIS_LIB \ --with-Metis-include=$METIS_INCLUDE \ --with-Tecio-lib=$TECIO_LIB \ --with-Tecio-include=$TECIO_INCLUDE \ --enable-metis=$METIS [root@tamnun HiFiLES-solver-master]# ./configure_run.sh checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes <<< Configuring library with Metis support >>> ./configure: line 3027: AX_TLS: command not found checking for /usr/lib64/atlas/libcblas.a... yes checking for /usr/lib64/atlas/libatlas.a... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking for style of include used by make... GNU checking dependency style of mpicxx... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1966080 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... mpicxx -E checking for ld used by mpicxx... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -DPIC works... yes checking if mpicxx static flag -static works... no checking if mpicxx supports -c -o file.o... yes checking if mpicxx supports -c -o file.o... (cached) yes checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate configure: creating ./config.status config.status: creating lib/parmetis-4.0.2/Makefile config.status: creating lib/parmetis-4.0.2/metis/Makefile config.status: creating Makefile config.status: creating lib/Makefile config.status: creating obj/Makefile config.status: executing depfiles commands config.status: executing libtool commands Build Configuration Summary: ``` Source code location: /usr/local/HiFiLES-solver-master Install location: / Version: 1.0.0 Compiler: mpicxx Preprocessor flags: Compiler flags: -D_MPI Linker flags: BLAS support: YES MPI support: YES CUDA support: NO TecIO support: NO ``` # make Making all in lib make[1]: Entering directory `/usr/local/HiFiLES-solver-master/lib' Making all in parmetis-4.0.2/ make[2]: Entering directory`/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' Making all in metis/ make[3]: Entering directory `/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis' CC GKlib/libmetis_a-b64.o CC GKlib/libmetis_a-blas.o CC GKlib/libmetis_a-csr.o CC GKlib/libmetis_a-error.o CC GKlib/libmetis_a-evaluate.o CC GKlib/libmetis_a-fkvkselect.o CC GKlib/libmetis_a-fs.o CC GKlib/libmetis_a-getopt.o CC GKlib/libmetis_a-gkregex.o CC GKlib/libmetis_a-htable.o CC GKlib/libmetis_a-io.o CC GKlib/libmetis_a-itemsets.o CC GKlib/libmetis_a-mcore.o CC GKlib/libmetis_a-memory.o CC GKlib/libmetis_a-omp.o CC GKlib/libmetis_a-pdb.o CC GKlib/libmetis_a-pqueue.o CC GKlib/libmetis_a-random.o CC GKlib/libmetis_a-seq.o CC GKlib/libmetis_a-sort.o CC GKlib/libmetis_a-string.o GKlib/string.c: In function ‘gk_str2time’: GKlib/string.c:506: warning: comparison between pointer and integer CC GKlib/libmetis_a-timers.o CC GKlib/libmetis_a-tokenizer.o CC GKlib/libmetis_a-util.o CC libmetis/libmetis_a-auxapi.o CC libmetis/libmetis_a-balance.o CC libmetis/libmetis_a-bucketsort.o CC libmetis/libmetis_a-checkgraph.o CC libmetis/libmetis_a-coarsen.o CC libmetis/libmetis_a-compress.o CC libmetis/libmetis_a-contig.o CC libmetis/libmetis_a-debug.o CC libmetis/libmetis_a-fm.o CC libmetis/libmetis_a-fortran.o CC libmetis/libmetis_a-frename.o CC libmetis/libmetis_a-gklib.o CC libmetis/libmetis_a-graph.o CC libmetis/libmetis_a-initpart.o CC libmetis/libmetis_a-kmetis.o CC libmetis/libmetis_a-kwayfm.o CC libmetis/libmetis_a-kwayrefine.o CC libmetis/libmetis_a-mcutil.o CC libmetis/libmetis_a-mesh.o CC libmetis/libmetis_a-meshpart.o CC libmetis/libmetis_a-minconn.o CC libmetis/libmetis_a-mincover.o CC libmetis/libmetis_a-mmd.o CC libmetis/libmetis_a-ometis.o CC libmetis/libmetis_a-options.o CC libmetis/libmetis_a-parmetis.o CC libmetis/libmetis_a-pmetis.o CC libmetis/libmetis_a-refine.o CC libmetis/libmetis_a-separator.o CC libmetis/libmetis_a-sfm.o CC libmetis/libmetis_a-srefine.o CC libmetis/libmetis_a-stat.o CC libmetis/libmetis_a-timing.o CC libmetis/libmetis_a-util.o CC libmetis/libmetis_a-wspace.o AR libmetis.a make[3]: Leaving directory`/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis' make[3]: Entering directory `/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' CC libparmetis/libparmetis_a-akwayfm.o CC libparmetis/libparmetis_a-ametis.o CC libparmetis/libparmetis_a-balancemylink.o CC libparmetis/libparmetis_a-comm.o CC libparmetis/libparmetis_a-csrmatch.o CC libparmetis/libparmetis_a-ctrl.o CC libparmetis/libparmetis_a-debug.o CC libparmetis/libparmetis_a-diffutil.o CC libparmetis/libparmetis_a-frename.o CC libparmetis/libparmetis_a-gkmetis.o CC libparmetis/libparmetis_a-gkmpi.o CC libparmetis/libparmetis_a-graph.o CC libparmetis/libparmetis_a-initbalance.o CC libparmetis/libparmetis_a-initmsection.o CC libparmetis/libparmetis_a-initpart.o CC libparmetis/libparmetis_a-kmetis.o CC libparmetis/libparmetis_a-kwayrefine.o CC libparmetis/libparmetis_a-match.o CC libparmetis/libparmetis_a-mdiffusion.o CC libparmetis/libparmetis_a-mesh.o CC libparmetis/libparmetis_a-mmetis.o CC libparmetis/libparmetis_a-move.o CC libparmetis/libparmetis_a-msetup.o CC libparmetis/libparmetis_a-node_refine.o CC libparmetis/libparmetis_a-ometis.o CC libparmetis/libparmetis_a-pspases.o CC libparmetis/libparmetis_a-redomylink.o CC libparmetis/libparmetis_a-remap.o CC libparmetis/libparmetis_a-renumber.o CC libparmetis/libparmetis_a-rmetis.o CC libparmetis/libparmetis_a-selectq.o CC libparmetis/libparmetis_a-serial.o CC libparmetis/libparmetis_a-stat.o CC libparmetis/libparmetis_a-timer.o CC libparmetis/libparmetis_a-util.o CC libparmetis/libparmetis_a-wave.o CC libparmetis/libparmetis_a-weird.o CC libparmetis/libparmetis_a-wspace.o CC libparmetis/libparmetis_a-xyzpart.o AR libparmetis.a make[3]: Leaving directory`/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' make[2]: Leaving directory `/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' Making all in parmetis-4.0.2/metis make[2]: Entering directory`/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory`/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis' make[2]: Entering directory `/usr/local/HiFiLES-solver-master/lib' make[2]: Nothing to be done for`all-am'. make[2]: Leaving directory `/usr/local/HiFiLES-solver-master/lib' make[1]: Leaving directory`/usr/local/HiFiLES-solver-master/lib' Making all in obj make[1]: Entering directory `/usr/local/HiFiLES-solver-master/obj' CXX ../src/___bin_HiFiLES-global.o g++: 1.0.0": No such file or directory : warning: missing terminating " character make[1]: *** [../src/___bin_HiFiLES-global.o] Error 1 make[1]: Leaving directory`/usr/local/HiFiLES-solver-master/obj' make: **\* [all-recursive] Error 1
mlopez14 commented 8 years ago

Sorry for the delay in the response; we were taken aback by the length of the message.

It seems to be a problem with how automake configured your compilation. Perhaps your compiler is not g++ but rather gcc or the like.

When you type g++ in your command line, do you get a message saying the command is non-existent?