[mpich-discuss] Newbie getting started question?
John Chludzinski
john.chludzinski at gmail.com
Fri Sep 14 22:10:58 CDT 2012
BTW, both libopa.so.1 and libmpl.so.1 are defined links within
/usr/lib/mpich2/lib/. And both -rpath or -rpath-link are "unrecognized
option" for gfortran.
On Fri, Sep 14, 2012 at 10:47 PM, John Chludzinski <
john.chludzinski at gmail.com> wrote:
> *$ mpif90 -o ex1 ex1.f95*
> /usr/bin/ld: warning: libopa.so.1, needed by
> /usr/lib/mpich2/lib/libmpichf90.so, not found (try using -rpath or
> -rpath-link)
> /usr/bin/ld: warning: libmpl.so.1, needed by
> /usr/lib/mpich2/lib/libmpichf90.so, not found (try using -rpath or
> -rpath-link)
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trfree'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_env2str'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trlevel'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trvalid'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trmalloc'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trspace'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_env2range'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trcalloc'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_env2int'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trdump'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_env2bool'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trstrdup'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trrealloc'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_TrSetMaxMem'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trinit'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trDebugLevel'
> /usr/lib/mpich2/lib/libmpich.so: undefined reference to `MPL_trid'
>
>
> On Fri, Sep 14, 2012 at 10:37 PM, John Chludzinski <
> john.chludzinski at gmail.com> wrote:
>
>> Just ran: yum install mpich2-devel
>>
>> # ls -l /usr/lib/mpich2/lib/
>> total 7484
>>
>> -rw-r--r--. 1 root root 25459 Jan 2 2012 clog2print.jar
>> -rw-r--r--. 1 root root 127339 Jan 2 2012 clog2TOdrawable.jar
>> -rw-r--r--. 1 root root 183747 Jan 2 2012 clog2TOslog2.jar
>> -rw-r--r--. 1 root root 17400 Jan 2 2012 clogprint.jar
>> -rw-r--r--. 1 root root 108290 Jan 2 2012 clogTOdrawable.jar
>> -rw-r--r--. 1 root root 164701 Jan 2 2012 clogTOslog2.jar
>> -rw-r--r--. 1 root root 2449314 Jan 2 2012 jumpshot.jar
>> -rw-r--r--. 1 root root 7140 Jan 2 2012 jumpshot_launcher.jar
>> -rw-r--r--. 1 root root 16278 Jan 2 2012 libampe.a
>> lrwxrwxrwx. 1 root root 16 Sep 14 22:33 libfmpich.so ->
>> libfmpich.so.3.3
>>
>> lrwxrwxrwx. 1 root root 16 Sep 14 16:20 libfmpich.so.3 ->
>> libfmpich.so.3.3
>> -rwxr-xr-x. 1 root root 121604 Jan 2 2012 libfmpich.so.3.3
>> -rw-r--r--. 1 root root 271832 Jan 2 2012 liblmpe.a
>> -rw-r--r--. 1 root root 237292 Jan 2 2012 libmpe.a
>> -rw-r--r--. 1 root root 182660 Jan 2 2012 libmpe_collchk.a
>> -rw-r--r--. 1 root root 36448 Jan 2 2012 libmpe_f2cmpi.a
>> -rw-r--r--. 1 root root 219056 Jan 2 2012 libmpe_nompi.a
>> -rw-r--r--. 1 root root 20776 Jan 2 2012 libmpe_nompi_null.a
>> -rw-r--r--. 1 root root 10356 Jan 2 2012 libmpe_null.a
>> lrwxrwxrwx. 1 root root 18 Sep 14 22:33 libmpichcxx.so ->
>> libmpichcxx.so.3.3
>>
>> lrwxrwxrwx. 1 root root 18 Sep 14 16:20 libmpichcxx.so.3 ->
>> libmpichcxx.so.3.3
>> -rwxr-xr-x. 1 root root 116756 Jan 2 2012 libmpichcxx.so.3.3
>> lrwxrwxrwx. 1 root root 18 Sep 14 22:33 libmpichf90.so ->
>> libmpichf90.so.3.3
>>
>> lrwxrwxrwx. 1 root root 18 Sep 14 16:20 libmpichf90.so.3 ->
>> libmpichf90.so.3.3
>> -rwxr-xr-x. 1 root root 5644 Jan 2 2012 libmpichf90.so.3.3
>> lrwxrwxrwx. 1 root root 15 Sep 14 22:33 libmpich.so ->
>> libmpich.so.3.3
>>
>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libmpich.so.3 ->
>> libmpich.so.3.3
>> -rwxr-xr-x. 1 root root 1861652 Jan 2 2012 libmpich.so.3.3
>> lrwxrwxrwx. 1 root root 15 Sep 14 22:33 libmpl.so -> libmpl.so.1.1.0
>>
>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libmpl.so.1 ->
>> libmpl.so.1.1.0
>> -rwxr-xr-x. 1 root root 15612 Jan 2 2012 libmpl.so.1.1.0
>> lrwxrwxrwx. 1 root root 15 Sep 14 22:33 libopa.so -> libopa.so.1.0.0
>>
>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libopa.so.1 ->
>> libopa.so.1.0.0
>> -rwxr-xr-x. 1 root root 3940 Jan 2 2012 libopa.so.1.0.0
>> -rw-r--r--. 1 root root 86000 Jan 2 2012 libtmpe.a
>>
>> -rw-r--r--. 1 root root 265485 Jan 2 2012 logconvertor.jar
>> -rw-r--r--. 1 root root 10760 Jan 2 2012 mpe_prof.o
>> -rw-r--r--. 1 root root 173622 Jan 2 2012 slog2filter.jar
>> -rw-r--r--. 1 root root 136084 Jan 2 2012 slog2navigator.jar
>> -rw-r--r--. 1 root root 136091 Jan 2 2012 slog2printrecur.jar
>> -rw-r--r--. 1 root root 136086 Jan 2 2012 slog2printserial.jar
>> -rw-r--r--. 1 root root 261610 Jan 2 2012 slog2update205to206.jar
>> -rw-r--r--. 1 root root 67742 Jan 2 2012 traceprint.jar
>> drwxr-xr-x. 2 root root 4096 Sep 14 22:33 trace_rlog
>>
>> -rw-r--r--. 1 root root 124160 Jan 2 2012 traceTOslog2.jar
>>
>>
>> On Fri, Sep 14, 2012 at 8:08 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>>
>>> This package is missing the symlinks libmpich.so -> libmpich.so.3.3. Is
>>> there a separate mpich2-devel package?
>>>
>>> On Fri, Sep 14, 2012 at 6:57 PM, John Chludzinski <
>>> john.chludzinski at gmail.com> wrote:
>>>
>>>> $ ls -l /usr/lib/mpich2/lib
>>>> total 6412
>>>> -rw-r--r--. 1 root root 25459 Jan 2 2012 clog2print.jar
>>>> -rw-r--r--. 1 root root 127339 Jan 2 2012 clog2TOdrawable.jar
>>>> -rw-r--r--. 1 root root 183747 Jan 2 2012 clog2TOslog2.jar
>>>> -rw-r--r--. 1 root root 17400 Jan 2 2012 clogprint.jar
>>>> -rw-r--r--. 1 root root 108290 Jan 2 2012 clogTOdrawable.jar
>>>> -rw-r--r--. 1 root root 164701 Jan 2 2012 clogTOslog2.jar
>>>> -rw-r--r--. 1 root root 2449314 Jan 2 2012 jumpshot.jar
>>>> -rw-r--r--. 1 root root 7140 Jan 2 2012 jumpshot_launcher.jar
>>>> lrwxrwxrwx. 1 root root 16 Sep 14 16:20 libfmpich.so.3 ->
>>>> libfmpich.so.3.3
>>>> -rwxr-xr-x. 1 root root 121604 Jan 2 2012 libfmpich.so.3.3
>>>> lrwxrwxrwx. 1 root root 18 Sep 14 16:20 libmpichcxx.so.3 ->
>>>> libmpichcxx.so.3.3
>>>> -rwxr-xr-x. 1 root root 116756 Jan 2 2012 libmpichcxx.so.3.3
>>>> lrwxrwxrwx. 1 root root 18 Sep 14 16:20 libmpichf90.so.3 ->
>>>> libmpichf90.so.3.3
>>>> -rwxr-xr-x. 1 root root 5644 Jan 2 2012 libmpichf90.so.3.3
>>>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libmpich.so.3 ->
>>>> libmpich.so.3.3
>>>> -rwxr-xr-x. 1 root root 1861652 Jan 2 2012 libmpich.so.3.3
>>>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libmpl.so.1 ->
>>>> libmpl.so.1.1.0
>>>> -rwxr-xr-x. 1 root root 15612 Jan 2 2012 libmpl.so.1.1.0
>>>> lrwxrwxrwx. 1 root root 15 Sep 14 16:20 libopa.so.1 ->
>>>> libopa.so.1.0.0
>>>> -rwxr-xr-x. 1 root root 3940 Jan 2 2012 libopa.so.1.0.0
>>>> -rw-r--r--. 1 root root 265485 Jan 2 2012 logconvertor.jar
>>>> -rw-r--r--. 1 root root 10760 Jan 2 2012 mpe_prof.o
>>>> -rw-r--r--. 1 root root 173622 Jan 2 2012 slog2filter.jar
>>>> -rw-r--r--. 1 root root 136084 Jan 2 2012 slog2navigator.jar
>>>> -rw-r--r--. 1 root root 136091 Jan 2 2012 slog2printrecur.jar
>>>> -rw-r--r--. 1 root root 136086 Jan 2 2012 slog2printserial.jar
>>>> -rw-r--r--. 1 root root 261610 Jan 2 2012 slog2update205to206.jar
>>>> -rw-r--r--. 1 root root 67742 Jan 2 2012 traceprint.jar
>>>> -rw-r--r--. 1 root root 124160 Jan 2 2012 traceTOslog2.jar
>>>>
>>>>
>>>> $ mpif90 -show
>>>> gfortran -m32 -O2 -fPIC -Wl,-z,noexecstack -I/usr/include/mpich2-i386
>>>> -I/usr/include/mpich2-i386 -L/usr/lib/mpich2/lib -lmpichf90 -lmpichf90
>>>> -lmpich
>>>>
>>>> On Fri, Sep 14, 2012 at 7:54 PM, Jed Brown <jedbrown at mcs.anl.gov>wrote:
>>>>
>>>>> On Fri, Sep 14, 2012 at 6:41 PM, John Chludzinski <
>>>>> john.chludzinski at gmail.com> wrote:
>>>>>
>>>>>> MPICH2 Version: 1.4.1p1
>>>>>> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
>>>>>> MPICH2 Device: ch3:nemesis
>>>>>> MPICH2 configure: --build=i386-redhat-linux-gnu
>>>>>> --host=i386-redhat-linux-gnu --program-prefix=
>>>>>> --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr
>>>>>> --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc
>>>>>> --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib
>>>>>> --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib
>>>>>> --mandir=/usr/share/man --infodir=/usr/share/info --enable-sharedlibs=gcc
>>>>>> --enable-shared --enable-lib-depend --disable-rpath
>>>>>
>>>>>
>>>>> Because of this option, you will need
>>>>> LD_LIBRARY_PATH=/usr/lib/mpich2/lib to run executables.
>>>>>
>>>>>
>>>>>> --enable-fc --with-device=ch3:nemesis --with-pm=hydra:gforker
>>>>>> --sysconfdir=/etc/mpich2-i386 --includedir=/usr/include/mpich2-i386
>>>>>> --bindir=/usr/lib/mpich2/bin --libdir=/usr/lib/mpich2/lib
>>>>>
>>>>>
>>>>> According to the output you showed above, this option was either
>>>>> missed or the distribution packaged it differently on install. What system
>>>>> is this on? What is the output of
>>>>>
>>>>> $ ls -l /usr/lib/mpich2/lib
>>>>>
>>>>> $ mpif90 -show
>>>>>
>>>>>
>>>>>> --datadir=/usr/share/mpich2 --mandir=/usr/share/man/mpich2
>>>>>> --docdir=/usr/share/mpich2/doc --htmldir=/usr/share/mpich2/doc
>>>>>> --with-hwloc-prefix=system --with-java=/etc/alternatives/java_sdk
>>>>>> FC=gfortran F77=gfortran CFLAGS=-m32 -O2 -fPIC CXXFLAGS=-m32 -O2 -fPIC
>>>>>> FCFLAGS=-m32 -O2 -fPIC FFLAGS=-m32 -O2 -fPIC LDFLAGS=-Wl,-z,noexecstack
>>>>>> MPICH2LIB_CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>>>>>> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables MPICH2LIB_CXXFLAGS=-O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables MPICH2LIB_FCFLAGS=-O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables MPICH2LIB_FFLAGS=-O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables
>>>>>> MPICH2 CC: gcc -m32 -O2 -fPIC -O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables -O2
>>>>>> MPICH2 CXX: c++ -m32 -O2 -fPIC -O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables -O2
>>>>>> MPICH2 F77: gfortran -m32 -O2 -fPIC -O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables -O2
>>>>>> MPICH2 FC: gfortran -m32 -O2 -fPIC -O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
>>>>>> -fasynchronous-unwind-tables -O2
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 14, 2012 at 7:31 PM, Jed Brown <jedbrown at mcs.anl.gov>wrote:
>>>>>>
>>>>>>> On Fri, Sep 14, 2012 at 6:23 PM, John Chludzinski <
>>>>>>> john.chludzinski at gmail.com> wrote:
>>>>>>>
>>>>>>>> Why is this installation of MPICH2 ("compiler wrapper") trying to
>>>>>>>> statically link against "mpichf90" and "mpich" ? Versus dynamically link
>>>>>>>> against the shared object files in the lib directory.
>>>>>>>>
>>>>>>>
>>>>>>> It's not trying to "statically link", it's just trying to link. The
>>>>>>> correct path is not being specified, but we'd have to see output of
>>>>>>> mpich2version to say for sure. It's a waste of time to speculate.
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> How do I get the compiler wrapper to recognize this ?
>>>>>>>>
>>>>>>>> I assume I need to define: LD_LIBRARY_PATH=/usr/lib/mpich2/lib/ ?
>>>>>>>>
>>>>>>>
>>>>>>> This problem comes sooner.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> mpich-discuss mailing list mpich-discuss at mcs.anl.gov
>>>>>>> To manage subscription options or unsubscribe:
>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> mpich-discuss mailing list mpich-discuss at mcs.anl.gov
>>>>>> To manage subscription options or unsubscribe:
>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> mpich-discuss mailing list mpich-discuss at mcs.anl.gov
>>>>> To manage subscription options or unsubscribe:
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>>>>>
>>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>
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>>
>
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