xxirii
commented
5 years ago Dear Flavorenti,
I think your HDF5 environment is even not set in fact. I do not see any variable or path related to HDF5 in your environment.
First, can you check that you do not have a module called hdf5 in addition to the strange intel hdf5 module you have now.
Then, ensure that hdf5 is correctly set for Smilei :
export PATH=${where hdf5 is located}/hdf5/bin:${PATH}
export LD_LIBRARY_PATH=${where hdf5 is located}/hdf5/lib:${LD_LIBRARY_PATH}
export HDF5_ROOT_DIR=${where hdf5 is located}/hdf5Usually, the modules provide environment variable such as HDF5_ROOT_DIR or HDF5_HOME_DIR for instance that points to where it is installed.
If your system has no parallel hdf5, then you should consider to install it yourself. This is very easy in fact.
You can follow this page just for HDF5: http://www.maisondelasimulation.fr/smilei/install_linux.html
flavorenti
jderouillat
Good morning, I'm trying to install the latest version on Smilei (4.1) on the cluster here in Nice (website Nice supercomputer). But I'm encountering troubles with that, this is the list of the modules I've loaded before the installation:
############################################### [flavorenti@castor ~]$ module list Currently Loaded Modulefiles: 1) userspace/OCA 5) intel/compilers/2019.1.053 2) gnurt/8.3 6) intel/tbb/2019.1.053 3) mpi/2019.1.053 7) intel2019/hdf5/1.10.5-mpi 4) intel/mkl/2019.1.053 8) intel/python3/2019.1.053 ##################################################
So I see the most important stuff is there (python, MPI and HDF5), but when running the make command I get the following error:
############################################### [flavorenti@castor Smilei-4.1]$ make Unknown smilei version Compiling src/Collisions/Collisions.cpp src/Collisions/Collisions.cpp(366): error: identifier "H5Pset_fapl_mpio" is undefined H5Pset_fapl_mpio(file_access, MPI_COMM_WORLD, MPI_INFO_NULL); ^
src/Collisions/Collisions.cpp(383): error: identifier "H5Pset_dxpl_mpio" is undefined H5Pset_dxpl_mpio(transfer, H5FD_MPIO_COLLECTIVE); ^
compilation aborted for src/Collisions/Collisions.cpp (code 2) make: *** [build/src/Collisions/Collisions.o] Error 2 #######################################################
So it seems HDF5 is not enabled for parallelization... but this module has been installed with MPI (as the name says). I have to say that I haven't added any lines to the ~/.bashrc. Anyways I hope you can help me and I'm attaching other useful information concerning installation commands:
##################################################### [flavorenti@castor Smilei-4.1]$ git describe --all --long fatal: Not a git repository (or any parent up to mount point /beegfs) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). ########################################################
##################################################### [flavorenti@castor Smilei-4.1]$ make config=verbose Unknown smilei version Compiling src/Collisions/Collisions.cpp mpicxx -D__VERSION=\"??-??\" -D_VECTO -std=c++11 -Wall -Isrc -Isrc/Checkpoint -Isrc/SmileiMPI -Isrc/Pusher -Isrc/MultiphotonBreitWheeler -Isrc/Ionization -Isrc/Interpolator -Isrc/ElectroMagn -Isrc/Field -Isrc/Profiles -Isrc/Radiation -Isrc/Diagnostic -Isrc/Python -Isrc/ElectroMagnSolver -Isrc/Projector -Isrc/Params -Isrc/Tools -Isrc/DomainDecomposition -Isrc/picsar_interface -Isrc/ElectroMagnBC -Isrc/Collisions -Isrc/Species -Isrc/MovWindow -Isrc/Patch -Ibuild/src/Python -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_VECTO -O3 -g -fopenmp -D_OMP -c src/Collisions/Collisions.cpp -o build/src/Collisions/Collisions.o src/Collisions/Collisions.cpp(366): error: identifier "H5Pset_fapl_mpio" is undefined H5Pset_fapl_mpio(file_access, MPI_COMM_WORLD, MPI_INFO_NULL); ^
src/Collisions/Collisions.cpp(383): error: identifier "H5Pset_dxpl_mpio" is undefined H5Pset_dxpl_mpio(transfer, H5FD_MPIO_COLLECTIVE); ^
compilation aborted for src/Collisions/Collisions.cpp (code 2) make: *** [build/src/Collisions/Collisions.o] Error 2 #####################################################
################################################### [flavorenti@castor Smilei-4.1]$ make env Unknown smilei version SMILEICXX : mpicxx PYTHONEXE : python MPIVERSION : VERSION : ??-?? OPENMP_FLAG : -fopenmp -D_OMP HDF5_ROOT_DIR : SITEDIR : /beegfs/home/flavorenti/.local/lib/python3.6/site-packages PY_CXXFLAGS : -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION PY_LDFLAGS : -lpython3.6m -lpthread -ldl -lutil -lrt -lm -Xlinker -export-dynamic CXXFLAGS : -D__VERSION=\"??-??\" -D_VECTO -std=c++11 -Wall -Isrc -Isrc/Checkpoint -Isrc/SmileiMPI -Isrc/Pusher -Isrc/MultiphotonBreitWheeler -Isrc/Ionization -Isrc/Interpolator -Isrc/ElectroMagn -Isrc/Field -Isrc/Profiles -Isrc/Radiation -Isrc/Diagnostic -Isrc/Python -Isrc/ElectroMagnSolver -Isrc/Projector -Isrc/Params -Isrc/Tools -Isrc/DomainDecomposition -Isrc/picsar_interface -Isrc/ElectroMagnBC -Isrc/Collisions -Isrc/Species -Isrc/MovWindow -Isrc/Patch -Ibuild/src/Python -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/site-packages/numpy/core/include -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_VECTO -O3 -g -fopenmp -D_OMP LDFLAGS : -lhdf5 -lpython3.6m -lpthread -ldl -lutil -lrt -lm -Xlinker -export-dynamic -lm -fopenmp -D_OMP ###################################################
#################################################### [flavorenti@castor Smilei-4.1]$ echo $LD_LIBRARY_PATH /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib:/trinity/shared/OCA/softs/hdf5-1.10.5-intel19-mpi/lib:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/tbb/lib/intel64/gcc4.7:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/ipp/lib/intel64:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/compiler/lib/intel64:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/release_mt:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/mpi/intel64/libfabric/lib:/trinity/shared/apps/170135/x86_64/intel-2019.1/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib:/trinity/shared/OCA/softs/gnurt-8.3/lib64 ###############################################
############################################ [flavorenti@castor Smilei-4.1]$ python -m sysconfig Platform: "linux-x86_64" Python version: "3.6" Current installation scheme: "posix_prefix"
Paths: data = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" include = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m" platinclude = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m" platlib = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/site-packages" platstdlib = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6" purelib = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/site-packages" scripts = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/bin" stdlib = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6"
Variables: ABIFLAGS = "m" AC_APPLE_UNIVERSAL_BUILD = "0" AIX_GENUINE_CPLUSPLUS = "0" ANDROID_API_LEVEL = "0" AR = "ar" ARFLAGS = "rc" BASECFLAGS = "-Wno-unused-result -Wsign-compare" BASECPPFLAGS = "" BASEMODLIBS = "" BINDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/bin" BINLIBDEST = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6" BLDLIBRARY = "-L. -lpython3.6m" BLDSHARED = "gcc -pthread -shared -L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed -z noexecstack -z relro -z now -fstack-protector" BUILDEXE = "" BUILDPYTHON = "python" BUILD_GNU_TYPE = "x86_64-pc-linux-gnu" BYTESTR_DEPS = "\" CC = "gcc -pthread" CCSHARED = "-fPIC" CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC" CFLAGSFORSHARED = "-fPIC" CFLAGS_ALIASING = "" CFLAGS_NODIST = "" CONFIGFILES = "configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in" CONFIGURE_CFLAGS = "-Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC" CONFIGURE_CFLAGS_NODIST = "-std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers" CONFIGURE_CPPFLAGS = "-I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" CONFIGURE_LDFLAGS = "-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed" CONFIG_ARGS = "'--enable-shared' '--enable-ipv6' '--with-ensurepip=no' '--prefix=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3' '--with-tcltk-includes=-I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include' '--with-tcltk-libs=-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -ltcl8.6 -ltk8.6' 'CPPFLAGS=-I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include' 'LDFLAGS=-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed' 'CFLAGS=-Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC' 'PKG_CONFIG_PATH=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/pkgconfig'" CONFINCLUDEDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" CONFINCLUDEPY = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m" COREPYTHONPATH = ":" COVERAGE_INFO = "/workdir/conda-build/python_1539372461953/work/coverage.info" COVERAGE_REPORT = "/workdir/conda-build/python_1539372461953/work/lcov-report" COVERAGE_REPORT_OPTIONS = "--no-branch-coverage --title "CPython lcov report"" CPPFLAGS = "-I. -I./Include -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" CXX = "g++ -pthread" DESTDIRS = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3 /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6 /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/lib-dynload" DESTLIB = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6" DESTPATH = "" DESTSHARED = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/lib-dynload" DFLAGS = "" DIRMODE = "755" DIST = "README ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in Include Lib Misc Ext-dummy" DISTDIRS = "Include Lib Misc Ext-dummy" DISTFILES = "README ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in" DLINCLDIR = "." DLLLIBRARY = "" DOUBLE_IS_ARM_MIXED_ENDIAN_IEEE754 = "0" DOUBLE_IS_BIG_ENDIAN_IEEE754 = "0" DOUBLE_IS_LITTLE_ENDIAN_IEEE754 = "1" DTRACE = "" DTRACE_DEPS = "\" DTRACE_HEADERS = "" DTRACE_OBJS = "" DYNLOADFILE = "dynload_shlib.o" ENABLE_IPV6 = "1" ENSUREPIP = "no" EXE = "" EXEMODE = "755" EXTRAMACHDEPPATH = "" EXTRATESTOPTS = "" EXTRA_CFLAGS = "" EXT_SUFFIX = ".cpython-36m-x86_64-linux-gnu.so" FILEMODE = "644" FLOCK_NEEDS_LIBBSD = "0" GETPGRP_HAVE_ARG = "0" GETTIMEOFDAY_NO_TZ = "0" GITBRANCH = "" GITTAG = "" GITVERSION = "" GNULD = "yes" HAVE_ACCEPT4 = "1" HAVE_ACOSH = "1" HAVE_ADDRINFO = "1" HAVE_ALARM = "1" HAVE_ALIGNED_REQUIRED = "0" HAVE_ALLOCA_H = "1" HAVE_ALTZONE = "0" HAVE_ASINH = "1" HAVE_ASM_TYPES_H = "1" HAVE_ATANH = "1" HAVE_BIND_TEXTDOMAIN_CODESET = "1" HAVE_BLUETOOTH_BLUETOOTH_H = "0" HAVE_BLUETOOTH_H = "0" HAVE_BROKEN_MBSTOWCS = "0" HAVE_BROKEN_NICE = "0" HAVE_BROKEN_PIPE_BUF = "0" HAVE_BROKEN_POLL = "0" HAVE_BROKEN_POSIX_SEMAPHORES = "0" HAVE_BROKEN_PTHREAD_SIGMASK = "0" HAVE_BROKEN_SEM_GETVALUE = "0" HAVE_BROKEN_UNSETENV = "0" HAVE_BUILTIN_ATOMIC = "1" HAVE_CHFLAGS = "0" HAVE_CHOWN = "1" HAVE_CHROOT = "1" HAVE_CLOCK = "1" HAVE_CLOCK_GETRES = "1" HAVE_CLOCK_GETTIME = "1" HAVE_CLOCK_SETTIME = "1" HAVE_COMPUTED_GOTOS = "1" HAVE_CONFSTR = "1" HAVE_CONIO_H = "0" HAVE_COPYSIGN = "1" HAVE_CRYPT_H = "1" HAVE_CTERMID = "1" HAVE_CTERMID_R = "0" HAVE_CURSES_FILTER = "1" HAVE_CURSES_H = "1" HAVE_CURSES_HAS_KEY = "1" HAVE_CURSES_IMMEDOK = "1" HAVE_CURSES_IS_PAD = "0" HAVE_CURSES_IS_TERM_RESIZED = "1" HAVE_CURSES_RESIZETERM = "1" HAVE_CURSES_RESIZE_TERM = "1" HAVE_CURSES_SYNCOK = "1" HAVE_CURSES_TYPEAHEAD = "1" HAVE_CURSES_USE_ENV = "1" HAVE_CURSES_WCHGAT = "1" HAVE_DECL_ISFINITE = "1" HAVE_DECL_ISINF = "1" HAVE_DECL_ISNAN = "1" HAVE_DECL_RTLD_DEEPBIND = "1" HAVE_DECL_RTLD_GLOBAL = "1" HAVE_DECL_RTLD_LAZY = "1" HAVE_DECL_RTLD_LOCAL = "1" HAVE_DECL_RTLD_NODELETE = "1" HAVE_DECL_RTLD_NOLOAD = "1" HAVE_DECL_RTLD_NOW = "1" HAVE_DECL_TZNAME = "0" HAVE_DEVICE_MACROS = "1" HAVE_DEV_PTC = "0" HAVE_DEV_PTMX = "1" HAVE_DIRECT_H = "0" HAVE_DIRENT_D_TYPE = "1" HAVE_DIRENT_H = "1" HAVE_DIRFD = "1" HAVE_DLFCN_H = "1" HAVE_DLOPEN = "1" HAVE_DUP2 = "1" HAVE_DUP3 = "1" HAVE_DYNAMIC_LOADING = "1" HAVE_ENDIAN_H = "1" HAVE_EPOLL = "1" HAVE_EPOLL_CREATE1 = "1" HAVE_ERF = "1" HAVE_ERFC = "1" HAVE_ERRNO_H = "1" HAVE_EXECV = "1" HAVE_EXPM1 = "1" HAVE_FACCESSAT = "1" HAVE_FCHDIR = "1" HAVE_FCHMOD = "1" HAVE_FCHMODAT = "1" HAVE_FCHOWN = "1" HAVE_FCHOWNAT = "1" HAVE_FCNTL_H = "1" HAVE_FDATASYNC = "1" HAVE_FDOPENDIR = "1" HAVE_FEXECVE = "1" HAVE_FINITE = "1" HAVE_FLOCK = "1" HAVE_FORK = "1" HAVE_FORKPTY = "1" HAVE_FPATHCONF = "1" HAVE_FSEEK64 = "0" HAVE_FSEEKO = "1" HAVE_FSTATAT = "1" HAVE_FSTATVFS = "1" HAVE_FSYNC = "1" HAVE_FTELL64 = "0" HAVE_FTELLO = "1" HAVE_FTIME = "1" HAVE_FTRUNCATE = "1" HAVE_FUTIMENS = "1" HAVE_FUTIMES = "1" HAVE_FUTIMESAT = "1" HAVE_GAI_STRERROR = "1" HAVE_GAMMA = "1" HAVE_GCC_ASM_FOR_MC68881 = "0" HAVE_GCC_ASM_FOR_X64 = "1" HAVE_GCC_ASM_FOR_X87 = "1" HAVE_GCC_UINT128_T = "1" HAVE_GETADDRINFO = "1" HAVE_GETC_UNLOCKED = "1" HAVE_GETENTROPY = "0" HAVE_GETGROUPLIST = "1" HAVE_GETGROUPS = "1" HAVE_GETHOSTBYNAME = "0" HAVE_GETHOSTBYNAME_R = "1" HAVE_GETHOSTBYNAME_R_3_ARG = "0" HAVE_GETHOSTBYNAME_R_5_ARG = "0" HAVE_GETHOSTBYNAME_R_6_ARG = "1" HAVE_GETITIMER = "1" HAVE_GETLOADAVG = "1" HAVE_GETLOGIN = "1" HAVE_GETNAMEINFO = "1" HAVE_GETPAGESIZE = "1" HAVE_GETPEERNAME = "1" HAVE_GETPGID = "1" HAVE_GETPGRP = "1" HAVE_GETPID = "1" HAVE_GETPRIORITY = "1" HAVE_GETPWENT = "1" HAVE_GETRANDOM = "0" HAVE_GETRANDOM_SYSCALL = "0" HAVE_GETRESGID = "1" HAVE_GETRESUID = "1" HAVE_GETSID = "1" HAVE_GETSPENT = "1" HAVE_GETSPNAM = "1" HAVE_GETTIMEOFDAY = "1" HAVE_GETWD = "1" HAVE_GLIBC_MEMMOVE_BUG = "0" HAVE_GRP_H = "1" HAVE_HSTRERROR = "1" HAVE_HTOLE64 = "1" HAVE_HYPOT = "1" HAVE_IEEEFP_H = "0" HAVE_IF_NAMEINDEX = "1" HAVE_INET_ATON = "1" HAVE_INET_PTON = "1" HAVE_INITGROUPS = "1" HAVE_INTTYPES_H = "1" HAVE_IO_H = "0" HAVE_IPA_PURE_CONST_BUG = "0" HAVE_KILL = "1" HAVE_KILLPG = "1" HAVE_KQUEUE = "0" HAVE_LANGINFO_H = "1" HAVE_LARGEFILE_SUPPORT = "0" HAVE_LCHFLAGS = "0" HAVE_LCHMOD = "0" HAVE_LCHOWN = "1" HAVE_LGAMMA = "1" HAVE_LIBDL = "1" HAVE_LIBDLD = "0" HAVE_LIBIEEE = "0" HAVE_LIBINTL_H = "1" HAVE_LIBREADLINE = "0" HAVE_LIBRESOLV = "0" HAVE_LIBSENDFILE = "0" HAVE_LIBUTIL_H = "0" HAVE_LINK = "1" HAVE_LINKAT = "1" HAVE_LINUX_CAN_BCM_H = "0" HAVE_LINUX_CAN_H = "1" HAVE_LINUX_CAN_RAW_FD_FRAMES = "0" HAVE_LINUX_CAN_RAW_H = "1" HAVE_LINUX_NETLINK_H = "1" HAVE_LINUX_RANDOM_H = "1" HAVE_LINUX_TIPC_H = "1" HAVE_LOCKF = "1" HAVE_LOG1P = "1" HAVE_LOG2 = "1" HAVE_LONG_DOUBLE = "1" HAVE_LSTAT = "1" HAVE_LUTIMES = "1" HAVE_MAKEDEV = "1" HAVE_MBRTOWC = "1" HAVE_MEMMOVE = "1" HAVE_MEMORY_H = "1" HAVE_MEMRCHR = "1" HAVE_MKDIRAT = "1" HAVE_MKFIFO = "1" HAVE_MKFIFOAT = "1" HAVE_MKNOD = "1" HAVE_MKNODAT = "1" HAVE_MKTIME = "1" HAVE_MMAP = "1" HAVE_MREMAP = "1" HAVE_NCURSES_H = "1" HAVE_NDIR_H = "0" HAVE_NETPACKET_PACKET_H = "1" HAVE_NET_IF_H = "1" HAVE_NICE = "1" HAVE_OPENAT = "1" HAVE_OPENPTY = "1" HAVE_PATHCONF = "1" HAVE_PAUSE = "1" HAVE_PIPE2 = "1" HAVE_PLOCK = "0" HAVE_POLL = "1" HAVE_POLL_H = "1" HAVE_POSIX_FADVISE = "1" HAVE_POSIX_FALLOCATE = "1" HAVE_PREAD = "1" HAVE_PRLIMIT = "0" HAVE_PROCESS_H = "0" HAVE_PROTOTYPES = "1" HAVE_PTHREAD_ATFORK = "1" HAVE_PTHREAD_DESTRUCTOR = "0" HAVE_PTHREAD_H = "1" HAVE_PTHREAD_INIT = "0" HAVE_PTHREAD_KILL = "1" HAVE_PTHREAD_SIGMASK = "1" HAVE_PTY_H = "1" HAVE_PUTENV = "1" HAVE_PWRITE = "1" HAVE_READLINK = "1" HAVE_READLINKAT = "1" HAVE_READV = "1" HAVE_REALPATH = "1" HAVE_RENAMEAT = "1" HAVE_RL_APPEND_HISTORY = "0" HAVE_RL_CALLBACK = "0" HAVE_RL_CATCH_SIGNAL = "0" HAVE_RL_COMPLETION_APPEND_CHARACTER = "0" HAVE_RL_COMPLETION_DISPLAY_MATCHES_HOOK = "0" HAVE_RL_COMPLETION_MATCHES = "0" HAVE_RL_COMPLETION_SUPPRESS_APPEND = "0" HAVE_RL_PRE_INPUT_HOOK = "0" HAVE_RL_RESIZE_TERMINAL = "0" HAVE_ROUND = "1" HAVE_SCHED_GET_PRIORITY_MAX = "1" HAVE_SCHED_H = "1" HAVE_SCHED_RR_GET_INTERVAL = "1" HAVE_SCHED_SETAFFINITY = "1" HAVE_SCHED_SETPARAM = "1" HAVE_SCHED_SETSCHEDULER = "1" HAVE_SELECT = "1" HAVE_SEM_GETVALUE = "1" HAVE_SEM_OPEN = "1" HAVE_SEM_TIMEDWAIT = "1" HAVE_SEM_UNLINK = "1" HAVE_SENDFILE = "1" HAVE_SETEGID = "1" HAVE_SETEUID = "1" HAVE_SETGID = "1" HAVE_SETGROUPS = "1" HAVE_SETHOSTNAME = "1" HAVE_SETITIMER = "1" HAVE_SETLOCALE = "1" HAVE_SETPGID = "1" HAVE_SETPGRP = "1" HAVE_SETPRIORITY = "1" HAVE_SETREGID = "1" HAVE_SETRESGID = "1" HAVE_SETRESUID = "1" HAVE_SETREUID = "1" HAVE_SETSID = "1" HAVE_SETUID = "1" HAVE_SETVBUF = "1" HAVE_SHADOW_H = "1" HAVE_SIGACTION = "1" HAVE_SIGALTSTACK = "1" HAVE_SIGINTERRUPT = "1" HAVE_SIGNAL_H = "1" HAVE_SIGPENDING = "1" HAVE_SIGRELSE = "1" HAVE_SIGTIMEDWAIT = "1" HAVE_SIGWAIT = "1" HAVE_SIGWAITINFO = "1" HAVE_SNPRINTF = "1" HAVE_SOCKADDR_ALG = "0" HAVE_SOCKADDR_SA_LEN = "0" HAVE_SOCKADDR_STORAGE = "1" HAVE_SOCKETPAIR = "1" HAVE_SPAWN_H = "1" HAVE_SSIZE_T = "1" HAVE_STATVFS = "1" HAVE_STAT_TV_NSEC = "1" HAVE_STAT_TV_NSEC2 = "0" HAVE_STDARG_PROTOTYPES = "1" HAVE_STDINT_H = "1" HAVE_STDLIB_H = "1" HAVE_STD_ATOMIC = "0" HAVE_STRDUP = "1" HAVE_STRFTIME = "1" HAVE_STRINGS_H = "1" HAVE_STRING_H = "1" HAVE_STRLCPY = "0" HAVE_STROPTS_H = "0" HAVE_STRUCT_PASSWD_PW_GECOS = "1" HAVE_STRUCT_PASSWD_PW_PASSWD = "1" HAVE_STRUCT_STAT_ST_BIRTHTIME = "0" HAVE_STRUCT_STAT_ST_BLKSIZE = "1" HAVE_STRUCT_STAT_ST_BLOCKS = "1" HAVE_STRUCT_STAT_ST_FLAGS = "0" HAVE_STRUCT_STAT_ST_GEN = "0" HAVE_STRUCT_STAT_ST_RDEV = "1" HAVE_STRUCT_TM_TM_ZONE = "1" HAVE_SYMLINK = "1" HAVE_SYMLINKAT = "1" HAVE_SYNC = "1" HAVE_SYSCONF = "1" HAVE_SYSEXITS_H = "1" HAVE_SYS_AUDIOIO_H = "0" HAVE_SYS_BSDTTY_H = "0" HAVE_SYS_DEVPOLL_H = "0" HAVE_SYS_DIR_H = "0" HAVE_SYS_ENDIAN_H = "0" HAVE_SYS_EPOLL_H = "1" HAVE_SYS_EVENT_H = "0" HAVE_SYS_FILE_H = "1" HAVE_SYS_IOCTL_H = "1" HAVE_SYS_KERN_CONTROL_H = "0" HAVE_SYS_LOADAVG_H = "0" HAVE_SYS_LOCK_H = "0" HAVE_SYS_MKDEV_H = "0" HAVE_SYS_MODEM_H = "0" HAVE_SYS_NDIR_H = "0" HAVE_SYS_PARAM_H = "1" HAVE_SYS_POLL_H = "1" HAVE_SYS_RANDOM_H = "0" HAVE_SYS_RESOURCE_H = "1" HAVE_SYS_SELECT_H = "1" HAVE_SYS_SENDFILE_H = "1" HAVE_SYS_SOCKET_H = "1" HAVE_SYS_STATVFS_H = "1" HAVE_SYS_STAT_H = "1" HAVE_SYS_SYSCALL_H = "1" HAVE_SYS_SYSMACROS_H = "1" HAVE_SYS_SYS_DOMAIN_H = "0" HAVE_SYS_TERMIO_H = "0" HAVE_SYS_TIMES_H = "1" HAVE_SYS_TIME_H = "1" HAVE_SYS_TYPES_H = "1" HAVE_SYS_UIO_H = "1" HAVE_SYS_UN_H = "1" HAVE_SYS_UTSNAME_H = "1" HAVE_SYS_WAIT_H = "1" HAVE_SYS_XATTR_H = "1" HAVE_TCGETPGRP = "1" HAVE_TCSETPGRP = "1" HAVE_TEMPNAM = "1" HAVE_TERMIOS_H = "1" HAVE_TERM_H = "1" HAVE_TGAMMA = "1" HAVE_TIMEGM = "1" HAVE_TIMES = "1" HAVE_TMPFILE = "1" HAVE_TMPNAM = "1" HAVE_TMPNAM_R = "1" HAVE_TM_ZONE = "1" HAVE_TRUNCATE = "1" HAVE_TZNAME = "0" HAVE_UCS4_TCL = "0" HAVE_UNAME = "1" HAVE_UNISTD_H = "1" HAVE_UNLINKAT = "1" HAVE_UNSETENV = "1" HAVE_USABLE_WCHAR_T = "0" HAVE_UTIL_H = "0" HAVE_UTIMENSAT = "1" HAVE_UTIMES = "1" HAVE_UTIME_H = "1" HAVE_WAIT3 = "1" HAVE_WAIT4 = "1" HAVE_WAITID = "1" HAVE_WAITPID = "1" HAVE_WCHAR_H = "1" HAVE_WCSCOLL = "1" HAVE_WCSFTIME = "1" HAVE_WCSXFRM = "1" HAVE_WMEMCMP = "1" HAVE_WORKING_TZSET = "1" HAVE_WRITEV = "1" HAVE_ZLIB_COPY = "1" HAVE__GETPTY = "0" HOST_GNU_TYPE = "x86_64-pc-linux-gnu" INCLDIRSTOMAKE = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m /trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m" INCLUDEDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" INCLUDEPY = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include/python3.6m" INSTALL = "/usr/bin/install -c" INSTALL_DATA = "/usr/bin/install -c -m 644" INSTALL_PROGRAM = "/usr/bin/install -c" INSTALL_SCRIPT = "/usr/bin/install -c" INSTALL_SHARED = "/usr/bin/install -c -m 555" INSTSONAME = "libpython3.6m.so.1.0" IO_H = "Modules/_io/_iomodule.h" IO_OBJS = "\" LDCXXSHARED = "g++ -pthread -shared" LDFLAGS = "-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed -z noexecstack -z relro -z now -fstack-protector" LDLAST = "" LDLIBRARY = "libpython3.6m.so" LDLIBRARYDIR = "" LDSHARED = "gcc -pthread -shared -L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed -z noexecstack -z relro -z now -fstack-protector" LDVERSION = "3.6m" LIBC = "" LIBDEST = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6" LIBDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib" LIBFFI_INCLUDEDIR = "" LIBM = "-lm" LIBOBJDIR = "Python/" LIBOBJS = "" LIBPC = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/pkgconfig" LIBPL = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/config-3.6m-x86_64-linux-gnu" LIBRARY = "libpython3.6m.a" LIBRARY_OBJS = "\" LIBRARY_OBJS_OMIT_FROZEN = "\" LIBS = "-lpthread -ldl -lutil -lrt" LIBSUBDIRS = "tkinter tkinter/test tkinter/test/test_tkinter \" LINKCC = "gcc -pthread" LINKFORSHARED = "-Xlinker -export-dynamic" LIPO_32BIT_FLAGS = "" LLVM_PROF_ERR = "no" LLVM_PROF_FILE = "" LLVM_PROF_MERGER = "true" LN = "ln" LOCALMODLIBS = "" LOG1P_DROPS_ZERO_SIGN = "0" MACHDEP = "linux" MACHDEPPATH = ":" MACHDEP_OBJS = "" MACHDESTLIB = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6" MACOSX_DEPLOYMENT_TARGET = "" MAINCC = "gcc -pthread" MAJOR_IN_MKDEV = "0" MAJOR_IN_SYSMACROS = "0" MAKESETUP = "./Modules/makesetup" MANDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/share/man" MKDIR_P = "/bin/mkdir -p" MODLIBS = "" MODNAMES = "_thread posix errno pwd _sre _codecs _weakref _functools _operator _collections itertools atexit _signal _stat time _locale _io zipimport faulthandler _tracemalloc _symtable xxsubtype" MODOBJS = "Modules/_threadmodule.o Modules/posixmodule.o Modules/errnomodule.o Modules/pwdmodule.o Modules/_sre.o Modules/_codecsmodule.o Modules/_weakref.o Modules/_functoolsmodule.o Modules/_operator.o Modules/_collectionsmodule.o Modules/itertoolsmodule.o Modules/atexitmodule.o Modules/signalmodule.o Modules/_stat.o Modules/timemodule.o Modules/_localemodule.o Modules/_iomodule.o Modules/iobase.o Modules/fileio.o Modules/bytesio.o Modules/bufferedio.o Modules/textio.o Modules/stringio.o Modules/zipimport.o Modules/faulthandler.o Modules/_tracemalloc.o Modules/hashtable.o Modules/symtablemodule.o Modules/xxsubtype.o" MODULE_OBJS = "\" MULTIARCH = "x86_64-linux-gnu" MULTIARCH_CPPFLAGS = "-DMULTIARCH=\"x86_64-linux-gnu\"" MVWDELCH_IS_EXPRESSION = "1" NO_AS_NEEDED = "-Wl,--no-as-needed" OBJECT_OBJS = "\" OPT = "-DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes" OTHER_LIBTOOL_OPT = "" PACKAGE_BUGREPORT = "0" PACKAGE_NAME = "0" PACKAGE_STRING = "0" PACKAGE_TARNAME = "0" PACKAGE_URL = "0" PACKAGE_VERSION = "0" PARSER_HEADERS = "\" PARSER_OBJS = "\ Parser/myreadline.o Parser/parsetok.o Parser/tokenizer.o" PGEN = "Parser/pgen" PGENOBJS = "\ \" PGOBJS = "\" PGO_PROF_GEN_FLAG = "-fprofile-generate" PGO_PROF_USE_FLAG = "-fprofile-use -fprofile-correction" PLATDIR = "" POBJS = "\" POSIX_SEMAPHORES_NOT_ENABLED = "0" PROFILE_TASK = "-m test.regrtest --pgo" PTHREAD_SYSTEM_SCHED_SUPPORTED = "1" PURIFY = "" PY3LIBRARY = "libpython3.so" PYLONG_BITS_IN_DIGIT = "0" PYTHON = "python" PYTHONFRAMEWORK = "" PYTHONFRAMEWORKDIR = "no-framework" PYTHONFRAMEWORKINSTALLDIR = "" PYTHONFRAMEWORKPREFIX = "" PYTHONPATH = ":" PYTHON_FOR_BUILD = "./python -E" PYTHON_FOR_REGEN = "python3.6" PYTHON_HEADERS = "\" PYTHON_OBJS = "\" PY_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC" PY_CFLAGS_NODIST = "-std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers" PY_CORE_CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -fstack-protector -O3 -fpic -fPIC -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -I. -I./Include -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include -fPIC -DPy_BUILD_CORE" PY_CPPFLAGS = "-I. -I./Include -I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" PY_FORMAT_SIZE_T = ""z"" PY_LDFLAGS = "-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -Wl,-rpath=/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib,--no-as-needed -z noexecstack -z relro -z now -fstack-protector" Py_DEBUG = "0" Py_ENABLE_SHARED = "1" Py_HASH_ALGORITHM = "0" QUICKTESTOPTS = "-x test_subprocess test_io test_lib2to3 \" RANLIB = "ranlib" READELF = "readelf" RESSRCDIR = "Mac/Resources/framework" RETSIGTYPE = "void" RUNSHARED = "LD_LIBRARY_PATH=/workdir/conda-build/python_1539372461953/work" SCRIPTDIR = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib" SETPGRP_HAVE_ARG = "0" SGI_ABI = "" SHELL = "/bin/sh" SHLIBS = "-lpthread -ldl -lutil -lrt" SHLIB_SUFFIX = ".so" SIGNED_RIGHT_SHIFT_ZERO_FILLS = "0" SITEPATH = "" SIZEOF_DOUBLE = "8" SIZEOF_FLOAT = "4" SIZEOF_FPOS_T = "16" SIZEOF_INT = "4" SIZEOF_LONG = "8" SIZEOF_LONG_DOUBLE = "16" SIZEOF_LONG_LONG = "8" SIZEOF_OFF_T = "8" SIZEOF_PID_T = "4" SIZEOF_PTHREAD_T = "8" SIZEOF_SHORT = "2" SIZEOF_SIZE_T = "8" SIZEOF_TIME_T = "8" SIZEOF_UINTPTR_T = "8" SIZEOF_VOID_P = "8" SIZEOF_WCHAR_T = "4" SIZEOF__BOOL = "1" SO = ".cpython-36m-x86_64-linux-gnu.so" SOABI = "cpython-36m-x86_64-linux-gnu" SRCDIRS = "Parser Objects Python Modules Programs" SRC_GDB_HOOKS = "./Tools/gdb/libpython.py" STDC_HEADERS = "1" STRICT_SYSV_CURSES = "/ Don't use ncurses extensions /" STRIPFLAG = "-s" SUBDIRS = "" SUBDIRSTOO = "Include Lib Misc" SYSLIBS = "-lm" SYS_SELECT_WITH_SYS_TIME = "1" TANH_PRESERVES_ZERO_SIGN = "1" TCLTK_INCLUDES = "-I/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/include" TCLTK_LIBS = "-L/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib -ltcl8.6 -ltk8.6" TESTOPTS = "" TESTPATH = "" TESTPYTHON = "LD_LIBRARY_PATH=/workdir/conda-build/python_1539372461953/work ./python" TESTPYTHONOPTS = "" TESTRUNNER = "LD_LIBRARY_PATH=/workdir/conda-build/python_1539372461953/work ./python ./Tools/scripts/run_tests.py" TESTTIMEOUT = "1200" THREADOBJ = "Python/thread.o" TIMEMODULE_LIB = "rt" TIME_WITH_SYS_TIME = "1" TM_IN_SYS_TIME = "0" UNICODE_DEPS = "\" UNIVERSALSDK = "" UPDATE_FILE = "python3.6 ./Tools/scripts/update_file.py" USE_COMPUTED_GOTOS = "0" USE_INLINE = "1" VERSION = "3.6" WANT_SIGFPE_HANDLER = "0" WINDOW_HAS_FLAGS = "1" WITH_DOC_STRINGS = "1" WITH_DTRACE = "0" WITH_DYLD = "0" WITH_LIBINTL = "0" WITH_NEXT_FRAMEWORK = "0" WITH_PYMALLOC = "1" WITH_THREAD = "1" WITH_VALGRIND = "0" X87_DOUBLE_ROUNDING = "0" XMLLIBSUBDIRS = "xml xml/dom xml/etree xml/parsers xml/sax" abiflags = "m" abs_builddir = "/workdir/conda-build/python_1539372461953/work" abs_srcdir = "/workdir/conda-build/python_1539372461953/work" base = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" datarootdir = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/share" exec_prefix = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" installed_base = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" installed_platbase = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" platbase = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" prefix = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3" projectbase = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/bin" py_version = "3.6.5" py_version_nodot = "36" py_version_short = "3.6" srcdir = "/trinity/shared/apps/170135/x86_64/intel-2019.1/intelpython3/lib/python3.6/config-3.6m-x86_64-linux-gnu" userbase = "/beegfs/home/flavorenti/.local" ##################################################
########################################### [flavorenti@castor Smilei-4.1]$ ldd smilei ldd: ./smilei: No such file or directory ##############################################