[OMPI devel] Error compiling
I am trying to compile the development version of openmpi obtained through svn yesterday, on a AMD64 computer running Ubuntu 12.10 (gcc 4.7.2) with valgrind-3.8.1 installed in /usr/local After ./autogen.pl. I ran configure: ../configure FC=gfortran --with-mpi-f90-size=medium --with-f90-max-array-dim=6 --with-valgrind=/usr/local however 'make all' exited with the error: make[2]: Entering directory `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' CC orte-clean.o CCLD orte-clean /usr/bin/ld: orte-clean.o: undefined reference to symbol 'opal_show_help_string' /usr/bin/ld: note: 'opal_show_help_string' is defined in DSO /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0 so try adding it to the linker command line /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[2]: *** [orte-clean] Error 1 make[2]: Leaving directory `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' make: *** [all-recursive] Error 1 I checked libopen-pal.so.0 using nm. Any suggestions to get the compilation working would be appreciated.
Re: [OMPI devel] Error compiling
Should be fixed with r27716. We had reorganized the linking a little while ago, and the person who did it thought that the indirect references would be resolved - i.e., that linking against liborte would automatically resolve any calls to functions in libopal since liborte is linked against libopal. Sadly, this wasn't true for the Mac, and it looks like it isn't true for Ubuntu either. Anyway, I resolved it by simply adding libopal to the list of libs for those tools. Let me know if it fixes this for you. On Dec 23, 2012, at 7:39 AM, R C wrote: > I am trying to compile the development version of openmpi obtained through > svn yesterday, on a AMD64 computer running Ubuntu 12.10 (gcc 4.7.2) with > valgrind-3.8.1 installed in /usr/local > > After ./autogen.pl. I ran configure: > ../configure FC=gfortran --with-mpi-f90-size=medium > --with-f90-max-array-dim=6 --with-valgrind=/usr/local > > however 'make all' exited with the error: > > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > CC orte-clean.o > CCLD orte-clean > /usr/bin/ld: orte-clean.o: undefined reference to symbol > 'opal_show_help_string' > /usr/bin/ld: note: 'opal_show_help_string' is defined in DSO > /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0 so try adding it to > the linker command line > /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0: could not read > symbols: Invalid operation > collect2: error: ld returned 1 exit status > make[2]: *** [orte-clean] Error 1 > make[2]: Leaving directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' > make: *** [all-recursive] Error 1 > > I checked libopen-pal.so.0 using nm. > > Any suggestions to get the compilation working would be appreciated. > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel
Re: [OMPI devel] Error compiling
I updated to r27716, reran autogen.pl and configure, but on running 'make all' I get this error: Making all in tools/orte-clean make[2]: Entering directory `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' CC orte-clean.o make[2]: *** No rule to make target `../../../orte/libopen-pal.la', needed by `orte-clean'. Stop. make[2]: Leaving directory `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' make: *** [all-recursive] Error 1 Thanks for looking into this. On Sun, Dec 23, 2012 at 10:56 AM, Ralph Castain wrote: > Should be fixed with r27716. We had reorganized the linking a little while > ago, and the person who did it thought that the indirect references would > be resolved - i.e., that linking against liborte would automatically > resolve any calls to functions in libopal since liborte is linked against > libopal. Sadly, this wasn't true for the Mac, and it looks like it isn't > true for Ubuntu either. > > Anyway, I resolved it by simply adding libopal to the list of libs for > those tools. Let me know if it fixes this for you. > > > On Dec 23, 2012, at 7:39 AM, R C wrote: > > I am trying to compile the development version of openmpi obtained through > svn yesterday, on a AMD64 computer running Ubuntu 12.10 (gcc 4.7.2) > with valgrind-3.8.1 installed in /usr/local > > After ./autogen.pl. I ran configure: > ../configure FC=gfortran --with-mpi-f90-size=medium > --with-f90-max-array-dim=6 --with-valgrind=/usr/local > > however 'make all' exited with the error: > > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > CC orte-clean.o > CCLD orte-clean > /usr/bin/ld: orte-clean.o: undefined reference to symbol > 'opal_show_help_string' > /usr/bin/ld: note: 'opal_show_help_string' is defined in DSO > /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0 so try adding it > to the linker command line > /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0: could not read > symbols: Invalid operation > collect2: error: ld returned 1 exit status > make[2]: *** [orte-clean] Error 1 > make[2]: Leaving directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' > make: *** [all-recursive] Error 1 > > I checked libopen-pal.so.0 using nm. > > Any suggestions to get the compilation working would be appreciated. > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel > > > > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel >
Re: [OMPI devel] Error compiling
Sorry about that - copy/paste error, combined with being in a hurry and not testing. Should be fixed now. On Dec 23, 2012, at 8:37 AM, R C wrote: > I updated to r27716, reran autogen.pl and configure, but on running 'make > all' I get this error: > > Making all in tools/orte-clean > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > CC orte-clean.o > make[2]: *** No rule to make target `../../../orte/libopen-pal.la', needed by > `orte-clean'. Stop. > make[2]: Leaving directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' > make: *** [all-recursive] Error 1 > > Thanks for looking into this. > > On Sun, Dec 23, 2012 at 10:56 AM, Ralph Castain wrote: > Should be fixed with r27716. We had reorganized the linking a little while > ago, and the person who did it thought that the indirect references would be > resolved - i.e., that linking against liborte would automatically resolve any > calls to functions in libopal since liborte is linked against libopal. Sadly, > this wasn't true for the Mac, and it looks like it isn't true for Ubuntu > either. > > Anyway, I resolved it by simply adding libopal to the list of libs for those > tools. Let me know if it fixes this for you. > > > On Dec 23, 2012, at 7:39 AM, R C wrote: > >> I am trying to compile the development version of openmpi obtained through >> svn yesterday, on a AMD64 computer running Ubuntu 12.10 (gcc 4.7.2) with >> valgrind-3.8.1 installed in /usr/local >> >> After ./autogen.pl. I ran configure: >> ../configure FC=gfortran --with-mpi-f90-size=medium >> --with-f90-max-array-dim=6 --with-valgrind=/usr/local >> >> however 'make all' exited with the error: >> >> make[2]: Entering directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> CC orte-clean.o >> CCLD orte-clean >> /usr/bin/ld: orte-clean.o: undefined reference to symbol >> 'opal_show_help_string' >> /usr/bin/ld: note: 'opal_show_help_string' is defined in DSO >> /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0 so try adding it to >> the linker command line >> /home/rc/Downloads/ompi/objd/opal/.libs/libopen-pal.so.0: could not read >> symbols: Invalid operation >> collect2: error: ld returned 1 exit status >> make[2]: *** [orte-clean] Error 1 >> make[2]: Leaving directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' >> make: *** [all-recursive] Error 1 >> >> I checked libopen-pal.so.0 using nm. >> >> Any suggestions to get the compilation working would be appreciated. >> ___ >> devel mailing list >> de...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/devel > > > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel > > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel
Re: [OMPI devel] Error compiling
Thanks again for looking into this. With r27717, 'make all' gives me the error: Making all in tools/ompi_info make[2]: Entering directory `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' CC ompi_info.o CC param.o ../../../../ompi/tools/ompi_info/param.c: In function ‘ompi_info_do_config’: ../../../../ompi/tools/ompi_info/param.c:238:17: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/param.c:252:17: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/param.c:259:17: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/param.c:271:13: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/param.c:274:13: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] CC components.o ../../../../ompi/tools/ompi_info/components.c: In function ‘ompi_info_register_components’: ../../../../ompi/tools/ompi_info/components.c:106:17: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/components.c:109:21: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/components.c:113:21: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] CC version.o ../../../../ompi/tools/ompi_info/version.c: In function ‘ompi_info_show_ompi_version’: ../../../../ompi/tools/ompi_info/version.c:125:13: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/version.c:134:13: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] ../../../../ompi/tools/ompi_info/version.c:137:13: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result [-Wunused-result] CCLD ompi_info /usr/bin/ld: version.o: undefined reference to symbol 'orte_info_type_orte' /usr/bin/ld: note: 'orte_info_type_orte' is defined in DSO /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0 so try adding it to the linker command line /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[2]: *** [ompi_info] Error 1 make[2]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi' make: *** [all-recursive] Error 1 On Sun, Dec 23, 2012 at 1:14 PM, Ralph Castain wrote: > Sorry about that - copy/paste error, combined with being in a hurry and > not testing. Should be fixed now. > > On Dec 23, 2012, at 8:37 AM, R C wrote: > > I updated to r27716, reran autogen.pl and configure, but on running 'make > all' I get this error: > > Making all in tools/orte-clean > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > CC orte-clean.o > make[2]: *** No rule to make target `../../../orte/libopen-pal.la', > needed by `orte-clean'. Stop. > make[2]: Leaving directory > `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' > make: *** [all-recursive] Error 1 > > Thanks for looking into this. > >
Re: [OMPI devel] Error compiling
Sigh - sorry about that. Guess we'll have to feel our way down the various tools. I've committed a fix that -should- resolve this for the rest of the tools in the OMPI layer. Please let me know how it works for you. Ralph On Dec 23, 2012, at 10:56 AM, R C wrote: > > Thanks again for looking into this. > With r27717, 'make all' gives me the error: > > Making all in tools/ompi_info > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' > CC ompi_info.o > CC param.o > ../../../../ompi/tools/ompi_info/param.c: In function ‘ompi_info_do_config’: > ../../../../ompi/tools/ompi_info/param.c:238:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:252:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:259:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:271:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:274:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CC components.o > ../../../../ompi/tools/ompi_info/components.c: In function > ‘ompi_info_register_components’: > ../../../../ompi/tools/ompi_info/components.c:106:17: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/components.c:109:21: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/components.c:113:21: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CC version.o > ../../../../ompi/tools/ompi_info/version.c: In function > ‘ompi_info_show_ompi_version’: > ../../../../ompi/tools/ompi_info/version.c:125:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/version.c:134:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/version.c:137:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CCLD ompi_info > /usr/bin/ld: version.o: undefined reference to symbol 'orte_info_type_orte' > /usr/bin/ld: note: 'orte_info_type_orte' is defined in DSO > /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0 so try adding it to > the linker command line > /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0: could not read > symbols: Invalid operation > collect2: error: ld returned 1 exit status > make[2]: *** [ompi_info] Error 1 > make[2]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi' > make: *** [all-recursive] Error 1 > > > On Sun, Dec 23, 2012 at 1:14 PM, Ralph Castain wrote: > Sorry about that - copy/paste error, combined with being in a hurry and not > testing. Should be fixed now. > > On Dec 23, 2012, at 8:37 AM, R C wrote: > >> I updated to r27716, reran autogen.pl and configure, but on running 'make >> all' I get this error: >> >> Making all in tools/orte-clean >> make[2]: Entering directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> CC orte-clean.o >> make[2]: *** No rule to make target `../../../orte/libopen-pal.la', needed >> by `orte-clean'. Stop. >> make[2]: Leaving directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' >> make: *** [all-recursive] Error 1 >> >> Thanks for looking into this. >> > > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel
Re: [OMPI devel] Error compiling
Thanks, r27719 compiles but I get an error when I try: $/usr/local/bin/ompi_info /usr/local/bin/ompi_info: symbol lookup error: /usr/local/bin/ompi_info: undefined symbol: mca_fbtl_base_components_opened and when I tried to compile a test program: $ mpicc -o hw hello.c mpicc: Symbol `opal_show_help' has different size in shared object, consider re-linking On Sun, Dec 23, 2012 at 2:55 PM, Ralph Castain wrote: > Sigh - sorry about that. Guess we'll have to feel our way down the various > tools. I've committed a fix that -should- resolve this for the rest of the > tools in the OMPI layer. Please let me know how it works for you. > > Ralph > > On Dec 23, 2012, at 10:56 AM, R C wrote: > > > Thanks again for looking into this. > With r27717, 'make all' gives me the error: > > Making all in tools/ompi_info > make[2]: Entering directory > `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' > CC ompi_info.o > CC param.o > ../../../../ompi/tools/ompi_info/param.c: In function > ‘ompi_info_do_config’: > ../../../../ompi/tools/ompi_info/param.c:238:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:252:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:259:17: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:271:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/param.c:274:13: warning: ignoring return > value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CC components.o > ../../../../ompi/tools/ompi_info/components.c: In function > ‘ompi_info_register_components’: > ../../../../ompi/tools/ompi_info/components.c:106:17: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/components.c:109:21: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/components.c:113:21: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CC version.o > ../../../../ompi/tools/ompi_info/version.c: In function > ‘ompi_info_show_ompi_version’: > ../../../../ompi/tools/ompi_info/version.c:125:13: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/version.c:134:13: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > ../../../../ompi/tools/ompi_info/version.c:137:13: warning: ignoring > return value of ‘asprintf’, declared with attribute warn_unused_result > [-Wunused-result] > CCLD ompi_info > /usr/bin/ld: version.o: undefined reference to symbol 'orte_info_type_orte' > /usr/bin/ld: note: 'orte_info_type_orte' is defined in DSO > /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0 so try adding it > to the linker command line > /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0: could not read > symbols: Invalid operation > collect2: error: ld returned 1 exit status > make[2]: *** [ompi_info] Error 1 > make[2]: Leaving directory > `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi' > make: *** [all-recursive] Error 1 > > > On Sun, Dec 23, 2012 at 1:14 PM, Ralph Castain wrote: > >> Sorry about that - copy/paste error, combined with being in a hurry and >> not testing. Should be fixed now. >> >> On Dec 23, 2012, at 8:37 AM, R C wrote: >> >> I updated to r27716, reran autogen.pl and configure, but on running >> 'make all' I get this error: >> >> Making all in tools/orte-clean >> make[2]: Entering directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> CC orte-clean.o >> make[2]: *** No rule to make target `../../../orte/libopen-pal.la', >> needed by `orte-clean'. Stop. >> make[2]: Leaving directory >> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' >> make: *** [all-recursive] Error 1 >> >> Thanks for looking into this. >> >> > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel > > > > ___ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel >
Re: [OMPI devel] Error compiling
Do you have your LD_LIBRARY_PATH set correctly? You want your prefix location to be at the front so you don't pickup something from the default system installation. On Dec 23, 2012, at 12:39 PM, R C wrote: > Thanks, r27719 compiles but I get an error when I try: > $/usr/local/bin/ompi_info > /usr/local/bin/ompi_info: symbol lookup error: /usr/local/bin/ompi_info: > undefined symbol: mca_fbtl_base_components_opened > > and when I tried to compile a test program: > $ mpicc -o hw hello.c > mpicc: Symbol `opal_show_help' has different size in shared object, consider > re-linking > > > > On Sun, Dec 23, 2012 at 2:55 PM, Ralph Castain wrote: > Sigh - sorry about that. Guess we'll have to feel our way down the various > tools. I've committed a fix that -should- resolve this for the rest of the > tools in the OMPI layer. Please let me know how it works for you. > > Ralph > > On Dec 23, 2012, at 10:56 AM, R C wrote: > >> >> Thanks again for looking into this. >> With r27717, 'make all' gives me the error: >> >> Making all in tools/ompi_info >> make[2]: Entering directory >> `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' >> CC ompi_info.o >> CC param.o >> ../../../../ompi/tools/ompi_info/param.c: In function ‘ompi_info_do_config’: >> ../../../../ompi/tools/ompi_info/param.c:238:17: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/param.c:252:17: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/param.c:259:17: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/param.c:271:13: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/param.c:274:13: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> CC components.o >> ../../../../ompi/tools/ompi_info/components.c: In function >> ‘ompi_info_register_components’: >> ../../../../ompi/tools/ompi_info/components.c:106:17: warning: ignoring >> return value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/components.c:109:21: warning: ignoring >> return value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/components.c:113:21: warning: ignoring >> return value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> CC version.o >> ../../../../ompi/tools/ompi_info/version.c: In function >> ‘ompi_info_show_ompi_version’: >> ../../../../ompi/tools/ompi_info/version.c:125:13: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/version.c:134:13: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> ../../../../ompi/tools/ompi_info/version.c:137:13: warning: ignoring return >> value of ‘asprintf’, declared with attribute warn_unused_result >> [-Wunused-result] >> CCLD ompi_info >> /usr/bin/ld: version.o: undefined reference to symbol 'orte_info_type_orte' >> /usr/bin/ld: note: 'orte_info_type_orte' is defined in DSO >> /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0 so try adding it to >> the linker command line >> /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0: could not read >> symbols: Invalid operation >> collect2: error: ld returned 1 exit status >> make[2]: *** [ompi_info] Error 1 >> make[2]: Leaving directory >> `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info' >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi' >> make: *** [all-recursive] Error 1 >> >> >> On Sun, Dec 23, 2012 at 1:14 PM, Ralph Castain wrote: >> Sorry about that - copy/paste error, combined with being in a hurry and not >> testing. Should be fixed now. >> >> On Dec 23, 2012, at 8:37 AM, R C wrote: >> >>> I updated to r27716, reran autogen.pl and configure, but on running 'make >>> all' I get this error: >>> >>> Making all in tools/orte-clean >>> make[2]: Entering directory >>> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >>> CC orte-clean.o >>> make[2]: *** No rule to make target `../../../orte/libopen-pal.la', needed >>> by `orte-clean'. Stop. >>> make[2]: Leaving directory >>> `/home/rc/Downloads/ompi/objd/orte/tools/orte-clean' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/orte' >>> make: *** [all-recursive] Error 1 >>> >>> Thanks for looking into this. >>> >> >>
Re: [OMPI devel] Error compiling
I put /usr/local/lib at the beginning of LD_LIBRARY_PATH and I get: $ ompi_info [RCAsus1:20105] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_errmgr_default: /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: orte_errmgr_base_output (ignored) [RCAsus1:20105] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_slurmd: /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class (ignored) [RCAsus1:20105] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_grpcomm_basic: /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: opal_profile_file (ignored) [RCAsus1:20105] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_cm: /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: orte_message_event_t_class (ignored) [RCAsus1:20105] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_linear: /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: orte_message_event_t_class (ignored) Package: Open MPI rc@RCAsus1 Distribution Open MPI: 1.9a1r27719 Open MPI repo revision: r27719 Open MPI release date: Unreleased developer copy Open RTE: 1.9a1r27719 and now when I try: $ mpicc -o hw hello.c it seems to compile, but from: $mpirun -np 4 hw RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_slurmd: /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_errmgr_default: /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: orte_errmgr_base_output (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_cm: /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: orte_message_event_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_linear: /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: orte_message_event_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_grpcomm_basic: /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: opal_profile_file (ignored) [RCAsus1:26668] *** Process received signal *** [RCAsus1:26668] Signal: Segmentation fault (11) [RCAsus1:26668] Signal code: (128) [RCAsus1:26668] Failing at address: (nil) [RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f0e31d54cb0] [RCAsus1:26668] [ 1] /usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) [0x7f0e2f720ca8] [RCAsus1:26668] [ 2] /usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba) [0x7f0e3226b09a] [RCAsus1:26668] [ 3] /usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626) [0x7f0e31fb97e6] [RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3) [0x7f0e31f87483] [RCAsus1:26668] [ 5] mpirun(orterun+0x10fb) [0x404b8d] [RCAsus1:26668] [ 6] mpirun(main+0x20) [0x4036ec] [RCAsus1:26668] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f0e319a776d] [RCAsus1:26668] [ 8] mpirun() [0x4035e9] [RCAsus1:26668] *** End of error message *** Segmentation fault (core dumped) 504:5 $ mpicc -o hw hello.c [04:37 PM][rc@RCAsus1] [~/Dropbox/tst] 505:6 $ mpirun -np 4 hw [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_ess_slurmd: /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_errmgr_default: /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: orte_errmgr_base_output (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_cm: /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: orte_message_event_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_routed_linear: /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: orte_message_event_t_class (ignored) [RCAsus1:26668] mca: base: component_find: unable to open /usr/local/lib/openmpi/mca_grpcomm_basic: /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: opal_profile_file (ignored) [RCAsus1:26668] *** Process received signal *** [RCAsus1:26668] Signal: Segmentation fault (11) [RCAsus1:26668] Signal code: (128) [RCAsus1:26668] Failing at address: (nil) [RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f0e31d54cb0] [RCAsus1:26668] [ 1] /usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) [0x7f0e2f720ca8] [RCAsus1:26668] [ 2] /usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba) [0x7f0e3226b09a] [RCAsus1:26668] [ 3] /usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626) [0x7f0e31fb97e6] [RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3) [
Re: [OMPI devel] Error compiling
Wow - strange. How was this configured? Something clearly is messed up as there is no such thing as a "basic" grpcomm module, or an ess "slurmd" module, etc. any more. My best guess is that you wound up installing this on top of an existing OMPI install, and have now created a massive library confusion problem. Try configuring it --with-prefix=, where foo is under your home directory. This will provide a clean place to install without confusion. Then put that location at the front of your path and ld_library_path - I suspect things will be okay from there. On Dec 23, 2012, at 1:43 PM, R C wrote: > I put /usr/local/lib at the beginning of LD_LIBRARY_PATH and I get: > $ ompi_info > [RCAsus1:20105] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_errmgr_default: > /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: > orte_errmgr_base_output (ignored) > [RCAsus1:20105] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_ess_slurmd: > /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class > (ignored) > [RCAsus1:20105] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_grpcomm_basic: > /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: > opal_profile_file (ignored) > [RCAsus1:20105] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_cm: > /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: > orte_message_event_t_class (ignored) > [RCAsus1:20105] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_linear: > /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: > orte_message_event_t_class (ignored) > Package: Open MPI rc@RCAsus1 Distribution > Open MPI: 1.9a1r27719 > Open MPI repo revision: r27719 >Open MPI release date: Unreleased developer copy > Open RTE: 1.9a1r27719 > > > and now when I try: >> $ mpicc -o hw hello.c > > it seems to compile, but from: > $mpirun -np 4 hw > RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_ess_slurmd: > /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class > (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_errmgr_default: > /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: > orte_errmgr_base_output (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_cm: > /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: > orte_message_event_t_class (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_linear: > /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: > orte_message_event_t_class (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_grpcomm_basic: > /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: > opal_profile_file (ignored) > [RCAsus1:26668] *** Process received signal *** > [RCAsus1:26668] Signal: Segmentation fault (11) > [RCAsus1:26668] Signal code: (128) > [RCAsus1:26668] Failing at address: (nil) > [RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f0e31d54cb0] > [RCAsus1:26668] [ 1] /usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) > [0x7f0e2f720ca8] > [RCAsus1:26668] [ 2] > /usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba) > [0x7f0e3226b09a] > [RCAsus1:26668] [ 3] > /usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626) > [0x7f0e31fb97e6] > [RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3) > [0x7f0e31f87483] > [RCAsus1:26668] [ 5] mpirun(orterun+0x10fb) [0x404b8d] > [RCAsus1:26668] [ 6] mpirun(main+0x20) [0x4036ec] > [RCAsus1:26668] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f0e319a776d] > [RCAsus1:26668] [ 8] mpirun() [0x4035e9] > [RCAsus1:26668] *** End of error message *** > Segmentation fault (core dumped) > > > > 504:5 $ mpicc -o hw hello.c > [04:37 PM][rc@RCAsus1] [~/Dropbox/tst] > 505:6 $ mpirun -np 4 hw > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_ess_slurmd: > /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class > (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_errmgr_default: > /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: > orte_errmgr_base_output (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_cm: > /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: > orte_message_event_t_class (ignored) > [RCAsus1:26668] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_routed_linear: > /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: > orte_
Re: [OMPI devel] Error compiling
I had originally installed v1.6.3 in /usr/local but had problems with it hanging on some commands. The installation of the development version in the same directory probably is the reason for the errors I am getting. I will do a clean install in a different directory. Thanks for your help. On Dec 23, 2012, at 5:28 PM, Ralph Castain wrote: > Wow - strange. How was this configured? > > Something clearly is messed up as there is no such thing as a "basic" grpcomm > module, or an ess "slurmd" module, etc. any more. My best guess is that you > wound up installing this on top of an existing OMPI install, and have now > created a massive library confusion problem. > > Try configuring it --with-prefix=, where foo is under your home > directory. This will provide a clean place to install without confusion. Then > put that location at the front of your path and ld_library_path - I suspect > things will be okay from there. > > > On Dec 23, 2012, at 1:43 PM, R C wrote: > >> I put /usr/local/lib at the beginning of LD_LIBRARY_PATH and I get: >> $ ompi_info >> [RCAsus1:20105] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_errmgr_default: >> /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: >> orte_errmgr_base_output (ignored) >> [RCAsus1:20105] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_ess_slurmd: >> /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class >> (ignored) >> [RCAsus1:20105] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_grpcomm_basic: >> /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: >> opal_profile_file (ignored) >> [RCAsus1:20105] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_routed_cm: >> /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: >> orte_message_event_t_class (ignored) >> [RCAsus1:20105] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_routed_linear: >> /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: >> orte_message_event_t_class (ignored) >> Package: Open MPI rc@RCAsus1 Distribution >> Open MPI: 1.9a1r27719 >> Open MPI repo revision: r27719 >>Open MPI release date: Unreleased developer copy >> Open RTE: 1.9a1r27719 >> >> >> and now when I try: >>> $ mpicc -o hw hello.c >> >> it seems to compile, but from: >> $mpirun -np 4 hw >> RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_ess_slurmd: >> /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class >> (ignored) >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_errmgr_default: >> /usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol: >> orte_errmgr_base_output (ignored) >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_routed_cm: >> /usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol: >> orte_message_event_t_class (ignored) >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_routed_linear: >> /usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol: >> orte_message_event_t_class (ignored) >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_grpcomm_basic: >> /usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol: >> opal_profile_file (ignored) >> [RCAsus1:26668] *** Process received signal *** >> [RCAsus1:26668] Signal: Segmentation fault (11) >> [RCAsus1:26668] Signal code: (128) >> [RCAsus1:26668] Failing at address: (nil) >> [RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) >> [0x7f0e31d54cb0] >> [RCAsus1:26668] [ 1] >> /usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) [0x7f0e2f720ca8] >> [RCAsus1:26668] [ 2] >> /usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba) >> [0x7f0e3226b09a] >> [RCAsus1:26668] [ 3] >> /usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626) >> [0x7f0e31fb97e6] >> [RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3) >> [0x7f0e31f87483] >> [RCAsus1:26668] [ 5] mpirun(orterun+0x10fb) [0x404b8d] >> [RCAsus1:26668] [ 6] mpirun(main+0x20) [0x4036ec] >> [RCAsus1:26668] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) >> [0x7f0e319a776d] >> [RCAsus1:26668] [ 8] mpirun() [0x4035e9] >> [RCAsus1:26668] *** End of error message *** >> Segmentation fault (core dumped) >> >> >> >> 504:5 $ mpicc -o hw hello.c >> [04:37 PM][rc@RCAsus1] [~/Dropbox/tst] >> 505:6 $ mpirun -np 4 hw >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_ess_slurmd: >> /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_nid_t_class >> (ignored) >> [RCAsus1:26668] mca: base: component_find: unable to open >> /usr/local/lib/openmpi/mca_errmgr_default: >> /usr/local/lib/o
