October 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] trouble installing
by Balaji, Pavan 30 Oct '14

30 Oct '14

> On Oct 29, 2014, at 11:50 PM, Michael Steffen <michael-steffen(a)utulsa.edu> wrote: > configure: error: **** Incompatible Fortran and C Object File Types! **** > F77 Object File Type produced by " " is : : cannot open `' (No such file or directory). > C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object x86_64. Please look through this link: http://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_I_get_a… — Pavan -- Pavan Balaji ✉️ http://www.mcs.anl.gov/~balaji _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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trouble installing
by Michael Steffen 29 Oct '14

29 Oct '14

I am having trouble installing mpich on my macbook pro. This is what my terminal window looks like when I try to install it at get stuck at the make part. What am I doing wrong? Last login: Wed Oct 29 22:36:42 on ttys000 Michaels-MacBook-Pro:~ michael-steffen$ cd /Users/michael-steffen/Desktop/mpich-3.1.3 Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ /Users/michael-steffen/Desktop/mpich-3.1.3/configure Configuring MPICH version 3.1.3 Running on system: Darwin Michaels-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 checking for icc... no checking for pgcc... no checking for xlc... no checking for xlC... no checking for pathcc... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... confdb/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking whether to enable maintainer-specific portions of Makefiles... yes checking for ar... ar checking the archiver (ar) interface... ar checking build system type... x86_64-apple-darwin13.4.0 checking host system type... x86_64-apple-darwin13.4.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... no 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 archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld 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 whether make supports nested variables... (cached) yes checking for icpc... no checking for pgCC... no checking for xlC... no checking for pathCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld checking how to hardcode library paths into programs... immediate checking for ifort... no checking for pgf90... no checking for pathf90... no checking for pathf95... no checking for xlf90... no checking for xlf95... no checking for xlf2003... no checking for gfortran... no checking for f90... no checking for epcf90... no checking for f95... no checking for fort... no checking for lf95... no checking for g95... no checking for ifc... no checking for efc... no checking for gfc... no checking whether we are using the GNU Fortran compiler... no checking whether accepts -g... no checking for ifort... no checking for pgf77... no checking for af77... no checking for xlf... no checking for frt... no checking for cf77... no checking for fort77... no checking for fl32... no checking for fort... no checking for ifc... no checking for efc... no checking for ftn... no checking for gfortran... no checking for f77... no checking for g77... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking hcoll/api/hcoll_api.h usability... no checking hcoll/api/hcoll_api.h presence... no checking for hcoll/api/hcoll_api.h... no checking for hcoll_init in -lhcoll... no configure: RUNNING PREREQ FOR ch3:nemesis checking for getpagesize... yes checking for getpagesize... (cached) yes configure: ===== configuring src/mpl ===== configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... confdb/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking the archiver (ar) interface... ar checking build system type... x86_64-apple-darwin13.4.0 checking host system type... x86_64-apple-darwin13.4.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... no 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 archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld 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 whether make supports nested variables... (cached) yes checking for an ANSI C-conforming const... yes checking for C/C++ restrict keyword... __restrict checking for inline... inline checking for variable argument list macro functionality... yes checking for gcov... gcov checking whether the compiler supports __typeof(variable)... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking search.h usability... yes checking search.h presence... yes checking for search.h... yes checking for sys/types.h... (cached) yes checking sys/uio.h usability... yes checking sys/uio.h presence... yes checking for sys/uio.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking valgrind.h usability... no checking valgrind.h presence... no checking for valgrind.h... no checking memcheck.h usability... no checking memcheck.h presence... no checking for memcheck.h... no checking valgrind/valgrind.h usability... no checking valgrind/valgrind.h presence... no checking for valgrind/valgrind.h... no checking valgrind/memcheck.h usability... no checking valgrind/memcheck.h presence... no checking for valgrind/memcheck.h... no checking helgrind.h usability... no checking helgrind.h presence... no checking for helgrind.h... no checking valgrind/helgrind.h usability... no checking valgrind/helgrind.h presence... no checking for valgrind/helgrind.h... no checking drd.h usability... no checking drd.h presence... no checking for drd.h... no checking valgrind/drd.h usability... no checking valgrind/drd.h presence... no checking for valgrind/drd.h... no checking whether the valgrind headers are broken or too old... yes checking for strdup... yes checking whether strdup needs a declaration... no checking for snprintf... yes checking whether snprintf needs a declaration... no checking for strncmp... yes checking whether strncmp needs a declaration... no checking for putenv... yes checking whether putenv needs a declaration... no checking whether __attribute__ allowed... yes checking whether __attribute__((format)) allowed... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating localdefs config.status: creating include/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing include/mplconfig.h commands config.status: creating include/mplconfig.h - prefix MPL for include/config.h defines configure: ===== done with src/mpl configure ===== configure: sourcing src/mpl/localdefs configure: ===== configuring src/openpa ===== configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --with-atomic-primitives=auto_allow_emulation --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... confdb/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking the archiver (ar) interface... ar checking build system type... x86_64-apple-darwin13.4.0 checking host system type... x86_64-apple-darwin13.4.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... no 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 archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.4.0 dyld 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 whether make supports nested variables... (cached) yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) gcc3 checking whether to enable assertions... yes checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking atomic.h usability... no checking atomic.h presence... no checking for atomic.h... no checking intrin.h usability... no checking intrin.h presence... no checking for intrin.h... no checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for C/C++ restrict keyword... __restrict checking for inline... inline checking for an ANSI C-conforming const... yes checking for pthread_create in -lpthread... yes checking for pthread_yield... no checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sched_yield... yes checking if 100 threads can be run at once... yes checking size of void *... 8 checking size of int... 4 checking whether __attribute__ allowed... yes checking whether __attribute__((format)) allowed... yes checking if compiler rejects bogus asm statements... yes checking for support for gcc x86/x86_64 primitives... yes checking for support for gcc x86 primitives for pre-Pentium 4... yes checking for support for gcc ia64 primitives... no checking for support for gcc PowerPC atomics... no checking for support for gcc ARM atomics... no checking for support for gcc SiCortex atomics... no checking for support for gcc atomic intrinsics... yes checking for support for Windows NT atomic intrinsics... no checking for support for Sun atomic operations library... no checking whether to enable strict fairness checks... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating openpa.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing src/opa_config.h commands config.status: creating src/opa_config.h - prefix OPA for src/config.h defines configure: ===== done with src/openpa configure ===== sourcing /Users/michael-steffen/Desktop/mpich-3.1.3/src/pm/hydra/mpichprereq checking whether the compiler defines __func__... yes checking whether the compiler defines __FUNC__... no checking whether the compiler sets __FUNCTION__... yes checking whether C compiler accepts option -O2... yes checking whether C compiler option -O2 works with an invalid prototype program... yes checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes checking for type of weak symbol alias support... no checking whether __attribute__ ((weak)) allowed... yes checking whether __attribute__ ((weak_import)) allowed... yes checking whether __attribute__((weak,alias(...))) allowed... no checking for shared library (esp. rpath) characteristics of CC... done (results in src/env/cc_shlib.conf) checking whether Fortran 77 compiler accepts option -O2... no checking how to get verbose linking output from ... configure: WARNING: compilation failed checking for Fortran 77 libraries of ... checking whether accepts the FLIBS found by autoconf... no checking for valid entries in FLIBS... checking whether gcc links with FLIBS found by autoconf... yes checking whether Fortran 77 and C objects are compatible... no checking for file... file configure: error: **** Incompatible Fortran and C Object File Types! **** F77 Object File Type produced by " " is : : cannot open `' (No such file or directory). C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object x86_64. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make make: *** No targets specified and no makefile found. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make |& tee m.txt -bash: syntax error near unexpected token `&' Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make | tee m.txt make: *** No targets specified and no makefile found. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make 2>&1 | tee m.txt make: *** No targets specified and no makefile found. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make clean make: *** No rule to make target `clean'. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 |& tee m.txt -bash: syntax error near unexpected token `&' Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 | tee m.txt make: *** No targets specified and no makefile found. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 tee m.txt make: *** No rule to make target `tee'. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 | tee m.txt make: *** No targets specified and no makefile found. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 tee m.txt make: *** No rule to make target `tee'. Stop. Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ Thanks, Mike -- Michael A. Steffen PhD. Candidate Department of Biological Sciences 800 S. Tucker Drive University of Tulsa Tulsa, OK 74104 Phone (708) 738-1491

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Re: [mpich-discuss] discuss Digest, Vol 24, Issue 35
by Latham, Robert J. 29 Oct '14

29 Oct '14

I probably just need to ensure lustre picked up all changes from common code. Can you confirm your code works if you prefix the filename with "ufs:" ? ==rob -- sent from a phone From: Sean Delaney <Sean.Delaney(a)tullowoil.com> Sent: Oct 29, 2014 9:54 AM To: discuss(a)mpich.org Cc: Latham, Robert J. Subject: RE: discuss Digest, Vol 24, Issue 35 Hi Rob, Yes, this is mpich-3.1.3, as downloaded from the website in the last 2 days. I was alerted to the buf_idx[] overflow by a failing assert statement, which checks for overflow when assigning values to buf_idx[]. I'm running on lustre. I can't provide my current code as a test case. I may be able to prepare something later, but I need to focus on making my code work first. These variables have type 'int', whereas something like 'size_t' or 'ADIO_Offset' might be more appropriate to store buffer offsets, where constraints are not known. Sean ----------------------- this is in the latest 3.1.3 MPICH? I thought I bumped up the size of buf_idx and related fields, though my test cases are meager at best. Do you have a test case? Which file system? ==rob ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] discuss Digest, Vol 24, Issue 35
by Sean Delaney 29 Oct '14

29 Oct '14

Hi Rob, Yes, this is mpich-3.1.3, as downloaded from the website in the last 2 days. I was alerted to the buf_idx[] overflow by a failing assert statement, which checks for overflow when assigning values to buf_idx[]. I'm running on lustre. I can't provide my current code as a test case. I may be able to prepare something later, but I need to focus on making my code work first. These variables have type 'int', whereas something like 'size_t' or 'ADIO_Offset' might be more appropriate to store buffer offsets, where constraints are not known. Sean ----------------------- this is in the latest 3.1.3 MPICH? I thought I bumped up the size of buf_idx and related fields, though my test cases are meager at best. Do you have a test case? Which file system? ==rob ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Bug: Adio 2GB Read/Write Size Limits
by Rob Latham 29 Oct '14

29 Oct '14

On 10/29/2014 04:10 AM, Sean Delaney wrote: > Hi, > > There seems to be a bug in ‘mpi/romio/adio’, relating to ‘buf_idx[]’ and associated variables, which are 32-bit signed integer arrays (or pointers to suitable allocations). As mentioned in the code comments, this type limits the size of the user’s arrays to 2GB. > > Recent fixes in other areas of mpich (e.g. trac issue 2010) have facilitated individual IO calls accessing >2GB of data. (In my case, this involved a large ‘MPI_Type_indexed’ file view.) Unfortunately, those fixes have exposed this limitation in adio. > > I briefly tried fixing this, but the changes grew beyond my available time. > > Regards, and thanks for the excellent work to date, this is in the latest 3.1.3 MPICH? I thought I bumped up the size of buf_idx and related fields, though my test cases are meager at best. Do you have a test case? Which file system? ==rob > > Sean > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Bug: Adio 2GB Read/Write Size Limits
by Sean Delaney 29 Oct '14

29 Oct '14

Hi, There seems to be a bug in ‘mpi/romio/adio’, relating to ‘buf_idx[]’ and associated variables, which are 32-bit signed integer arrays (or pointers to suitable allocations). As mentioned in the code comments, this type limits the size of the user’s arrays to 2GB. Recent fixes in other areas of mpich (e.g. trac issue 2010) have facilitated individual IO calls accessing >2GB of data. (In my case, this involved a large ‘MPI_Type_indexed’ file view.) Unfortunately, those fixes have exposed this limitation in adio. I briefly tried fixing this, but the changes grew beyond my available time. Regards, and thanks for the excellent work to date, Sean ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI process killed and SIGUSR1
by Wesley Bland 28 Oct '14

28 Oct '14

> On Oct 28, 2014, at 1:53 PM, Roy, Hirak <Hirak_Roy(a)mentor.com> wrote: > > Hi Wesley, > > Please check the client.c. There is explicit "assert" statement, which will terminate the client program abnormally. The server would be waiting on a MPI_Recv at that moment and the receive never times out or completes. You’re right. I had missed that. > > Even I replace the assert with sleep (100) and then manually kill the client process by process-id, the result is same. > > Could you please let me know if a client is abnormally terminated, is there any way to detect that from server or not. Support for FT with dynamic processes right now is somewhat unstable in MPICH, so it’s possible that it doesn’t work. It’s not something that’s been thoroughly tested on our end yet. All of the FT stuff is still very experimental and is actually being actively replaced. In fact, from the version that you’ve been using (3.0.4) and the current master branch, there have been some pretty major changes, so I can’t be sure what the behavior was at that point. You’re welcome to try out the latest code from the nightly builds, but obviously those are pretty rough as well. Unfortunately, this is all pretty unexplored territory so I can’t make any guarantees about anything at this point, though I’m happy to hear about any problems you have in order to improve future versions. Thanks, Wesley > > Thanks, > Hirak > > > Ok. I don't see where you're killing a process. > > > > > On Oct 27, 2014, at 10:51 PM, Roy, Hirak <Hirak_Roy at mentor.com <https://lists.mpich.org/mailman/listinfo/discuss>> wrote: > > > > Hi Wesley, > > > > This is related to the FT problem. > > > > Thanks, > > Hirak > > > > > > Is this still related to your FT problems or is this a separate problem? > > > > Thanks, > > Wesley > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re : MPI process killed and SIGUSR1
by Roy, Hirak 28 Oct '14

28 Oct '14

Hi Wesley, Please check the client.c. There is explicit "assert" statement, which will terminate the client program abnormally. The server would be waiting on a MPI_Recv at that moment and the receive never times out or completes. Even I replace the assert with sleep (100) and then manually kill the client process by process-id, the result is same. Could you please let me know if a client is abnormally terminated, is there any way to detect that from server or not. Thanks, Hirak > Ok. I don't see where you're killing a process. > On Oct 27, 2014, at 10:51 PM, Roy, Hirak <Hirak_Roy at mentor.com<https://lists.mpich.org/mailman/listinfo/discuss>> wrote: > > Hi Wesley, > > This is related to the FT problem. > > Thanks, > Hirak > > > Is this still related to your FT problems or is this a separate problem? > > Thanks, > Wesley > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Problems in MPICH 3.1.3 installation in OSX 10.10 with ifort compiler and Xcode 6.1
by Alejandro de la Calle 28 Oct '14

28 Oct '14

Thank you. So I suppose that finally it is a problem with ifort. All the best, Alex > El 28/10/2014, a las 15:08, Wesley Bland <wbland(a)anl.gov> escribió: > > I can confirm that I’ve been building on Yosemite for a while as well, but I also don’t have the Intel compilers available. I’ll see if I can find a system where I can test this out. > >> On Oct 28, 2014, at 10:02 AM, Junchao Zhang <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> >> I don't have Intel compilers for Mac OSX. But I succeeded in building mpich 3.1.3 with Yosemite + Xcode 6.1 + gcc/gfortran 4.9. >> >> --Junchao Zhang >> >> On Mon, Oct 27, 2014 at 6:49 PM, Alejandro de la Calle <alejandrodelacallenegro(a)gmail.com <mailto:[email protected]>> wrote: >> Hi there, >> >> I am trying to build mpich 3.1.3. in a Mac OSX 10.10 Yosemite with Xcode 6.1 and intel compilers icc and ifort version 15.0.0 20140716. I get an error when I am building the installation. The error is the following: >> >> GEN lib/libpmpi.la <http://libpmpi.la/> >> ifort: command line warning #10006: ignoring unknown option '-force_load,src/mpl/.libs/libmpl.a' >> ifort: command line warning #10006: ignoring unknown option '-force_load,/Users/alejandrodelacallenegro/Downloads/mpich-3.1.3/src/openpa/src/.libs/libopa.a' >> ifort: command line warning #10006: ignoring unknown option '-force_load,src/mpi/romio/.libs/libpromio.a' >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: object: lib/.libs/libpmpi.a(initthread.o) malformed object (section contents at offset 0 with a size of 1056, overlaps Mach-O headers at offset 0 with a size of 768) >> >> I do not understand where the error come from, from the compiler or from libtool. I have also attached the outputs of the configuration and the build steps. >> >> Thanks for your time, >> >> Alex >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Problems in MPICH 3.1.3 installation in OSX 10.10 with ifort compiler and Xcode 6.1
by Wesley Bland 28 Oct '14

28 Oct '14

I can confirm that I’ve been building on Yosemite for a while as well, but I also don’t have the Intel compilers available. I’ll see if I can find a system where I can test this out. > On Oct 28, 2014, at 10:02 AM, Junchao Zhang <jczhang(a)mcs.anl.gov> wrote: > > I don't have Intel compilers for Mac OSX. But I succeeded in building mpich 3.1.3 with Yosemite + Xcode 6.1 + gcc/gfortran 4.9. > > --Junchao Zhang > > On Mon, Oct 27, 2014 at 6:49 PM, Alejandro de la Calle <alejandrodelacallenegro(a)gmail.com <mailto:[email protected]>> wrote: > Hi there, > > I am trying to build mpich 3.1.3. in a Mac OSX 10.10 Yosemite with Xcode 6.1 and intel compilers icc and ifort version 15.0.0 20140716. I get an error when I am building the installation. The error is the following: > > GEN lib/libpmpi.la <http://libpmpi.la/> > ifort: command line warning #10006: ignoring unknown option '-force_load,src/mpl/.libs/libmpl.a' > ifort: command line warning #10006: ignoring unknown option '-force_load,/Users/alejandrodelacallenegro/Downloads/mpich-3.1.3/src/openpa/src/.libs/libopa.a' > ifort: command line warning #10006: ignoring unknown option '-force_load,src/mpi/romio/.libs/libpromio.a' > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: object: lib/.libs/libpmpi.a(initthread.o) malformed object (section contents at offset 0 with a size of 1056, overlaps Mach-O headers at offset 0 with a size of 768) > > I do not understand where the error come from, from the compiler or from libtool. I have also attached the outputs of the configuration and the build steps. > > Thanks for your time, > > Alex > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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