Thread: [Pympi-users] pyMPI interactively
Status: Alpha
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From: <db...@br...> - 2005-09-25 20:54:53
|
Greetings pyMPI-users, I'm working on some major upgrades, moving from pyMPI-1.3a1 running on RedHat 9 to pyMPI-2.4b3 running Fedore Core 4. I'm running lam-7.1.1-7.FC4. I'm using rsh on a private network. Once I got the prope= r version of rsh running on the machines (had to remove kerberos "rpm -e krb5-workstation"), most things generally work the same as before. For example: [dblank@bw40 mpi]$ mpirun -np 3 pyMPI sum.py 24499996500000 But, I used to be able to also run Python interactively. If I try with th= e -i flag, I get an error, or it hangs: [dblank@bw40 mpi]$ mpirun -np 3 pyMPI -i sum.py >>> 24499996500000 pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 Fatal Python error: PyThreadState_Get: no current thread -------------------------------------------------------------------------= ---- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 28595 failed on node n0 (10.0.0.40) due to signal 6. -------------------------------------------------------------------------= ---- Has something changed that prevents me from running interactively that way? I looked through the archives but didn't see anything. Maybe I have something configure incorrectly? Thanks for any hints, -Doug |
From: Julian C. <rjc...@cs...> - 2005-09-26 02:10:29
|
Does pyMPI run correctly when you startup interactively without running sum.py? i.e. in your case you should get: $ mpirun -np 3 pyMPI Python 2.4 (pyMPI 2.1b4) on sunos5 Type "help", "copyright", "credits" or "license" for more information. Python 2.4 (pyMPI 2.1b4) on sunos5 Type "help", "copyright", "credits" or "license" for more information. Python 2.4 (pyMPI 2.1b4) on sunos5 Type "help", "copyright", "credits" or "license" for more information. >>> Obviously my copy is a later version and on Solaris, but b3 should work correctly as well. Also, what is inside sum.py? Julian Cook -----Original Message----- From: pym...@li... [mailto:pym...@li...]On Behalf Of db...@br... Sent: Sunday, September 25, 2005 4:55 PM To: pym...@li... Subject: [Pympi-users] pyMPI interactively Greetings pyMPI-users, I'm working on some major upgrades, moving from pyMPI-1.3a1 running on RedHat 9 to pyMPI-2.4b3 running Fedore Core 4. I'm running lam-7.1.1-7.FC4. I'm using rsh on a private network. Once I got the proper version of rsh running on the machines (had to remove kerberos "rpm -e krb5-workstation"), most things generally work the same as before. For example: [dblank@bw40 mpi]$ mpirun -np 3 pyMPI sum.py 24499996500000 But, I used to be able to also run Python interactively. If I try with the -i flag, I get an error, or it hangs: [dblank@bw40 mpi]$ mpirun -np 3 pyMPI -i sum.py >>> 24499996500000 pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 Fatal Python error: PyThreadState_Get: no current thread ---------------------------------------------------------------------------- - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 28595 failed on node n0 (10.0.0.40) due to signal 6. ---------------------------------------------------------------------------- - Has something changed that prevents me from running interactively that way? I looked through the archives but didn't see anything. Maybe I have something configure incorrectly? Thanks for any hints, -Doug ------------------------------------------------------- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php _______________________________________________ Pympi-users mailing list Pym...@li... https://lists.sourceforge.net/lists/listinfo/pympi-users |
From: <db...@br...> - 2005-09-26 03:40:42
|
Thanks for some assistance. Details below. > Does pyMPI run correctly when you startup interactively without running > sum.py? > > i.e. in your case you should get: > > $ mpirun -np 3 pyMPI > > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > >>>> No, I can never get a prompt. Every time Python gets to where it should give the prompt, it either hangs till I control+c and gives the following error, or just gives the error immediately: pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 Fatal Python error: PyThreadState_Get: no current thread -------------------------------------------------------------------------= ---- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 944 failed on node n0 (10.0.0.1) due to signal 6. -------------------------------------------------------------------------= ---- I thought I'd try the unittests. I had to change line 231 in PyMPITest.py= to: cart =3D mpi.cart_create((1,int(mpi.procs)), (1,1), 0) and then they all ran without errors. So whatever is causing the crash, the unittests are testing for it. > Obviously my copy is a later version and on Solaris, but b3 should work > correctly as well. Also, what is inside sum.py? It doesn't really matter, as this happens with any python program, including an empty one, and the fractal.py example program. It must be that the Pythons are talking to each other correctly... if anyone has any ideas of other things to test/try please let me know. Thanks! -Doug > Julian Cook > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...]On Behalf Of > db...@br... > Sent: Sunday, September 25, 2005 4:55 PM > To: pym...@li... > Subject: [Pympi-users] pyMPI interactively > > > Greetings pyMPI-users, > > I'm working on some major upgrades, moving from pyMPI-1.3a1 running on > RedHat 9 to pyMPI-2.4b3 running Fedore Core 4. I'm running > lam-7.1.1-7.FC4. I'm using rsh on a private network. Once I got the pro= per > version of rsh running on the machines (had to remove kerberos "rpm -e > krb5-workstation"), most things generally work the same as before. For > example: > > [dblank@bw40 mpi]$ mpirun -np 3 pyMPI sum.py > 24499996500000 > > But, I used to be able to also run Python interactively. If I try with = the > -i flag, I get an error, or it hangs: > > [dblank@bw40 mpi]$ mpirun -np 3 pyMPI -i sum.py >>>> > 24499996500000 > pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 > Fatal Python error: PyThreadState_Get: no current thread > -----------------------------------------------------------------------= ----- > - > One of the processes started by mpirun has exited with a nonzero exit > code. This typically indicates that the process finished in error. > If your process did not finish in error, be sure to include a "return > 0" or "exit(0)" in your C code before exiting the application. > > PID 28595 failed on node n0 (10.0.0.40) due to signal 6. > -----------------------------------------------------------------------= ----- > - > > Has something changed that prevents me from running interactively that > way? I looked through the archives but didn't see anything. Maybe I hav= e > something configure incorrectly? > > Thanks for any hints, > > -Doug > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your v= ery > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.p= hp > _______________________________________________ > Pympi-users mailing list > Pym...@li... > https://lists.sourceforge.net/lists/listinfo/pympi-users > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your v= ery > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.p= hp > _______________________________________________ > Pympi-users mailing list > Pym...@li... > https://lists.sourceforge.net/lists/listinfo/pympi-users > |
From: Julian C. <rjc...@cs...> - 2005-09-26 04:12:52
|
I had this problem with pyMPI-2.0b0, at which point I was directed to use the CVS version, but the fix should be in b4. The other missing piece is the compile options, in that configure needs to be run: ./configure --prefix=/usr --with-isatty Obviously --prefix=/usr depends on where the ultimate install will be, but --with-isatty makes sure that the interactive console will work. There are some posts in November 2004 (see Julian cook, Mike Steder) that discuss a similar problem. There is another configure option with regard to Newlines, but normally that is not needed. Otherwise on Monday Pat Miller should be able to give better advice. Julian -----Original Message----- From: pym...@li... [mailto:pym...@li...]On Behalf Of db...@br... Sent: Sunday, September 25, 2005 11:41 PM To: rjc...@cs... Cc: db...@br...; pym...@li... Subject: RE: [Pympi-users] pyMPI interactively Thanks for some assistance. Details below. > Does pyMPI run correctly when you startup interactively without running > sum.py? > > i.e. in your case you should get: > > $ mpirun -np 3 pyMPI > > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > Python 2.4 (pyMPI 2.1b4) on sunos5 > Type "help", "copyright", "credits" or "license" for more information. > >>>> No, I can never get a prompt. Every time Python gets to where it should give the prompt, it either hangs till I control+c and gives the following error, or just gives the error immediately: pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 Fatal Python error: PyThreadState_Get: no current thread ---------------------------------------------------------------------------- - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 944 failed on node n0 (10.0.0.1) due to signal 6. ---------------------------------------------------------------------------- - I thought I'd try the unittests. I had to change line 231 in PyMPITest.py to: cart = mpi.cart_create((1,int(mpi.procs)), (1,1), 0) and then they all ran without errors. So whatever is causing the crash, the unittests are testing for it. > Obviously my copy is a later version and on Solaris, but b3 should work > correctly as well. Also, what is inside sum.py? It doesn't really matter, as this happens with any python program, including an empty one, and the fractal.py example program. It must be that the Pythons are talking to each other correctly... if anyone has any ideas of other things to test/try please let me know. Thanks! -Doug > Julian Cook > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...]On Behalf Of > db...@br... > Sent: Sunday, September 25, 2005 4:55 PM > To: pym...@li... > Subject: [Pympi-users] pyMPI interactively > > > Greetings pyMPI-users, > > I'm working on some major upgrades, moving from pyMPI-1.3a1 running on > RedHat 9 to pyMPI-2.4b3 running Fedore Core 4. I'm running > lam-7.1.1-7.FC4. I'm using rsh on a private network. Once I got the proper > version of rsh running on the machines (had to remove kerberos "rpm -e > krb5-workstation"), most things generally work the same as before. For > example: > > [dblank@bw40 mpi]$ mpirun -np 3 pyMPI sum.py > 24499996500000 > > But, I used to be able to also run Python interactively. If I try with the > -i flag, I get an error, or it hangs: > > [dblank@bw40 mpi]$ mpirun -np 3 pyMPI -i sum.py >>>> > 24499996500000 > pyMPI aborting on untrapped fatal signal 11 (SIGSEGV) on rank 0 > Fatal Python error: PyThreadState_Get: no current thread > -------------------------------------------------------------------------- -- > - > One of the processes started by mpirun has exited with a nonzero exit > code. This typically indicates that the process finished in error. > If your process did not finish in error, be sure to include a "return > 0" or "exit(0)" in your C code before exiting the application. > > PID 28595 failed on node n0 (10.0.0.40) due to signal 6. > -------------------------------------------------------------------------- -- > - > > Has something changed that prevents me from running interactively that > way? I looked through the archives but didn't see anything. Maybe I have > something configure incorrectly? > > Thanks for any hints, > > -Doug > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your very > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Pympi-users mailing list > Pym...@li... > https://lists.sourceforge.net/lists/listinfo/pympi-users > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your very > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Pympi-users mailing list > Pym...@li... > https://lists.sourceforge.net/lists/listinfo/pympi-users > ------------------------------------------------------- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php _______________________________________________ Pympi-users mailing list Pym...@li... https://lists.sourceforge.net/lists/listinfo/pympi-users |
From: <db...@br...> - 2005-09-26 12:42:11
|
Thanks, this sounds like it is the problem. However, when I compile it, I get the compilation error: pyMPI_isatty.c:48: error: syntax error before =91{=92 token /usr/bin/mpicc: No such file or directory make[1]: *** [pyMPI_isatty.o] Error 1 make[1]: Leaving directory `/home/setup/pyMPI-2.4b3' make: *** [all] Error 2 Here is what I get from configure: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets ${MAKE}... yes checking for ranlib... ranlib checking host overrides... no checking fatal error on cancel of isend (--with-bad-cancel)... no checking Assume stdin is interactive (--with-isatty)... yes checking Append a newline to prompt (--with-prompt-nl)... checking for mpcc... no checking for mpxlc... no checking for mpiicc... no checking for mpicc... mpicc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of mpicc... none checking for an ANSI C-conforming const... yes checking for mpicc is really C++... checking how to run the C preprocessor... mpicc -E checking for egrep... grep -E no checking for sed... /bin/sed checking for grep... /bin/grep checking for mpiCC... mpiCC checking whether we are using the GNU C++ compiler... yes checking whether mpiCC accepts -g... yes checking dependency style of mpiCC... none checking for mpicc... /usr/bin/mpicc checking for mpiCC... /usr/bin/mpiCC checking if /usr/bin/mpicc -E -w is a valid CPP... yes checking how to run the C preprocessor... /usr/bin/mpicc -E -w checking for --with-python... no checking executable /usr/bin/python2.4... yes checking for Python... /usr/bin/python2.4 checking for MPIRun.exe... no checking for mpirun... /usr/bin/mpirun checking for poe... no checking Python version 2.2 or higher... yes checking distutils?... yes checking distutils works... yes checking Numeric?... yes checking Numarray?... checking Python version string... 2.4 checking install prefix for /usr/bin/python2.4... /usr checking Prefix exists...... yes checking for python include location... /usr/include/python2.4 checking that include directory exists... yes checking for python library location... /usr/lib/python2.4/site-packages checking that lib directory is accessable... yes checking Python library... /usr/lib/python2.4 checking site.py... /usr/lib/python2.4/site.py checking site-packages... /usr/lib/python2.4/site-packages checking for python lib/config location... /usr/lib/python2.4/config checking that lib/config directory is accessable... yes checking libpython2.4.a is there... yes checking configuration Makefile is there... yes checking module configuration table is there... yes checking original Python there... yes checking for --with-includes... no checking for compiler based include directory... no checking MPI_COMPILE_FLAGS... no checking MPI_LD_FLAGS... no 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 mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes checking Python CC... gcc -pthread checking Python CFLAGS... -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=3D2 -fexceptions -m32 -march=3Di386 -mtune=3Dpentiu= m4 -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC checking Python INCLUDEPY... /usr/include/python2.4 checking Python OPT... -DNDEBUG -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=3D2 -fexceptions -m32 -march=3Di386 -mtune=3Dpentium4 -fasynchronous-unwind-t= ables -D_GNU_SOURCE -fPIC checking Python LDFLAGS... -L/usr/kerberos/lib checking Python LINKFORSHARED... -Xlinker -export-dynamic checking Python LDSHARED... gcc -pthread -shared checking Python BLDSHARED... gcc -pthread -shared checking Python LOCALMODLIBS... checking Python BASEMODLIBS... checking Python LIBS... -lpthread -ldl -lutil checking Python LDLAST... checking Python library options... -L/usr/lib/python2.4/config -lpython2.4 -L/usr/kerberos/lib -Xlinker -export-dynamic -lpthread -ldl= =20 -lutil checking for --with-dbfork... no checking for --with-debug... no checking python.exp file... no checking sysconf(_SC_NPROCESSORS_CONF)... yes checking for ANSI C header files... (cached) yes checking local processor count for testing... 2 checking for --with-libs... no checking for pow in -lm... yes checking for PyOS_StdioReadline... yes checking for setlinebuf... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking Python links as is... yes checking for MPI capability... yes checking for Py_ReadOnlyBytecodeFlag... no checking for MPI_Initialized()... yes checking for MPI_Finalized()... yes checking for MPI File operations (ROMIO)... yes checking for AIX dynamic load... no checking pm_util.h usability... no checking pm_util.h presence... no checking for pm_util.h... no checking for mpc_flush... no checking for mpc_isatty... no checking for Electric Fence enabled?... no I suspect that I am missing something (mpc_isatty?) and will poke around to see what I need to do to get it. -Doug > I had this problem with pyMPI-2.0b0, at which point I was directed to u= se > the CVS version, but the fix should be in b4. The other missing piece i= s > the > compile options, in that configure needs to be run: > > ./configure --prefix=3D/usr --with-isatty > > Obviously --prefix=3D/usr depends on where the ultimate install will be= , > but --with-isatty makes sure that the interactive console will work. Th= ere > are some posts in November 2004 (see Julian cook, Mike Steder) that > discuss > a similar problem. There is another configure option with regard to > Newlines, but normally that is not needed. Otherwise on Monday Pat Mill= er > should be able to give better advice. > > Julian |
From: Julian C. <rjc...@cs...> - 2005-09-26 14:52:11
|
Doug I'm not really sure why it's executing that section. From your configure you have: checking for pm_util.h... no checking for mpc_flush... no checking for mpc_isatty... no Which suggests that you should be compiling with the PYMPI_ISATTY section. If in doubt you could try compiling after removing the MPC section and test that. Otherwise let me know. I'm actually about 5 miles from you (Conshohocken), so we can compare the configure/ compile process over the phone if you get stuck. -----Original Message----- From: db...@br... [mailto:db...@br...] Sent: Monday, September 26, 2005 8:42 AM To: rjc...@cs... Cc: db...@br...; pym...@li... Subject: RE: [Pympi-users] pyMPI interactively Thanks, this sounds like it is the problem. However, when I compile it, I get the compilation error: pyMPI_isatty.c:48: error: syntax error before { token /usr/bin/mpicc: No such file or directory make[1]: *** [pyMPI_isatty.o] Error 1 make[1]: Leaving directory `/home/setup/pyMPI-2.4b3' make: *** [all] Error 2 Here is what I get from configure: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets ${MAKE}... yes checking for ranlib... ranlib checking host overrides... no checking fatal error on cancel of isend (--with-bad-cancel)... no checking Assume stdin is interactive (--with-isatty)... yes checking Append a newline to prompt (--with-prompt-nl)... checking for mpcc... no checking for mpxlc... no checking for mpiicc... no checking for mpicc... mpicc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of mpicc... none checking for an ANSI C-conforming const... yes checking for mpicc is really C++... checking how to run the C preprocessor... mpicc -E checking for egrep... grep -E no checking for sed... /bin/sed checking for grep... /bin/grep checking for mpiCC... mpiCC checking whether we are using the GNU C++ compiler... yes checking whether mpiCC accepts -g... yes checking dependency style of mpiCC... none checking for mpicc... /usr/bin/mpicc checking for mpiCC... /usr/bin/mpiCC checking if /usr/bin/mpicc -E -w is a valid CPP... yes checking how to run the C preprocessor... /usr/bin/mpicc -E -w checking for --with-python... no checking executable /usr/bin/python2.4... yes checking for Python... /usr/bin/python2.4 checking for MPIRun.exe... no checking for mpirun... /usr/bin/mpirun checking for poe... no checking Python version 2.2 or higher... yes checking distutils?... yes checking distutils works... yes checking Numeric?... yes checking Numarray?... checking Python version string... 2.4 checking install prefix for /usr/bin/python2.4... /usr checking Prefix exists...... yes checking for python include location... /usr/include/python2.4 checking that include directory exists... yes checking for python library location... /usr/lib/python2.4/site-packages checking that lib directory is accessable... yes checking Python library... /usr/lib/python2.4 checking site.py... /usr/lib/python2.4/site.py checking site-packages... /usr/lib/python2.4/site-packages checking for python lib/config location... /usr/lib/python2.4/config checking that lib/config directory is accessable... yes checking libpython2.4.a is there... yes checking configuration Makefile is there... yes checking module configuration table is there... yes checking original Python there... yes checking for --with-includes... no checking for compiler based include directory... no checking MPI_COMPILE_FLAGS... no checking MPI_LD_FLAGS... no 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 mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes checking Python CC... gcc -pthread checking Python CFLAGS... -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC checking Python INCLUDEPY... /usr/include/python2.4 checking Python OPT... -DNDEBUG -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC checking Python LDFLAGS... -L/usr/kerberos/lib checking Python LINKFORSHARED... -Xlinker -export-dynamic checking Python LDSHARED... gcc -pthread -shared checking Python BLDSHARED... gcc -pthread -shared checking Python LOCALMODLIBS... checking Python BASEMODLIBS... checking Python LIBS... -lpthread -ldl -lutil checking Python LDLAST... checking Python library options... -L/usr/lib/python2.4/config -lpython2.4 -L/usr/kerberos/lib -Xlinker -export-dynamic -lpthread -ldl -lutil checking for --with-dbfork... no checking for --with-debug... no checking python.exp file... no checking sysconf(_SC_NPROCESSORS_CONF)... yes checking for ANSI C header files... (cached) yes checking local processor count for testing... 2 checking for --with-libs... no checking for pow in -lm... yes checking for PyOS_StdioReadline... yes checking for setlinebuf... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking Python links as is... yes checking for MPI capability... yes checking for Py_ReadOnlyBytecodeFlag... no checking for MPI_Initialized()... yes checking for MPI_Finalized()... yes checking for MPI File operations (ROMIO)... yes checking for AIX dynamic load... no checking pm_util.h usability... no checking pm_util.h presence... no checking for pm_util.h... no checking for mpc_flush... no checking for mpc_isatty... no checking for Electric Fence enabled?... no I suspect that I am missing something (mpc_isatty?) and will poke around to see what I need to do to get it. -Doug > I had this problem with pyMPI-2.0b0, at which point I was directed to use > the CVS version, but the fix should be in b4. The other missing piece is > the > compile options, in that configure needs to be run: > > ./configure --prefix=/usr --with-isatty > > Obviously --prefix=/usr depends on where the ultimate install will be, > but --with-isatty makes sure that the interactive console will work. There > are some posts in November 2004 (see Julian cook, Mike Steder) that > discuss > a similar problem. There is another configure option with regard to > Newlines, but normally that is not needed. Otherwise on Monday Pat Miller > should be able to give better advice. > > Julian |
From: Douglas S. B. <db...@br...> - 2005-09-26 21:47:19
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Thanks, Julian, for the help and the offer. An update: I was able to compile pyMPI once I took out the offending lines, as you=20 suggested below. I actually had something that worked between two particular machines for=20 a short while, but I broke it again. I'm in the middle of upgrading the=20 entire cluster, so I'll make sure that I have everything the same on all=20 machines. There are so many places that can cause havoc: selinux, iptables, rsh,=20 lam, mpirun, python... Does anyone have a step-by-step check list for=20 getting up and running, especially on a Fedora Core 4 machine? I'll help=20 write it, if I ever get it working... -Doug Julian Cook wrote: > Doug >=20 > I'm not really sure why it's executing that section. From your configur= e you > have: >=20 > checking for pm_util.h... no > checking for mpc_flush... no > checking for mpc_isatty... no >=20 > Which suggests that you should be compiling with the PYMPI_ISATTY secti= on. >=20 > If in doubt you could try compiling after removing the MPC section and = test > that. Otherwise let me know. I'm actually about 5 miles from you > (Conshohocken), so we can compare the configure/ compile process over t= he > phone if you get stuck. >=20 > -----Original Message----- > From: db...@br... [mailto:db...@br...] > Sent: Monday, September 26, 2005 8:42 AM > To: rjc...@cs... > Cc: db...@br...; pym...@li... > Subject: RE: [Pympi-users] pyMPI interactively >=20 >=20 > Thanks, this sounds like it is the problem. However, when I compile it,= I > get the compilation error: >=20 > pyMPI_isatty.c:48: error: syntax error before =91{=92 token > /usr/bin/mpicc: No such file or directory > make[1]: *** [pyMPI_isatty.o] Error 1 > make[1]: Leaving directory `/home/setup/pyMPI-2.4b3' > make: *** [all] Error 2 >=20 > Here is what I get from configure: >=20 > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets ${MAKE}... yes > checking for ranlib... ranlib > checking host overrides... no > checking fatal error on cancel of isend (--with-bad-cancel)... no > checking Assume stdin is interactive (--with-isatty)... yes > checking Append a newline to prompt (--with-prompt-nl)... > checking for mpcc... no > checking for mpxlc... no > checking for mpiicc... no > checking for mpicc... mpicc > checking for C compiler default output... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... yes > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether mpicc accepts -g... yes > checking for mpicc option to accept ANSI C... none needed > checking for style of include used by make... GNU > checking dependency style of mpicc... none > checking for an ANSI C-conforming const... yes > checking for mpicc is really C++... checking how to run the C > preprocessor... mpicc -E > checking for egrep... grep -E > no > checking for sed... /bin/sed > checking for grep... /bin/grep > checking for mpiCC... mpiCC > checking whether we are using the GNU C++ compiler... yes > checking whether mpiCC accepts -g... yes > checking dependency style of mpiCC... none > checking for mpicc... /usr/bin/mpicc > checking for mpiCC... /usr/bin/mpiCC > checking if /usr/bin/mpicc -E -w is a valid CPP... yes > checking how to run the C preprocessor... /usr/bin/mpicc -E -w > checking for --with-python... no > checking executable /usr/bin/python2.4... yes > checking for Python... /usr/bin/python2.4 > checking for MPIRun.exe... no > checking for mpirun... /usr/bin/mpirun > checking for poe... no > checking Python version 2.2 or higher... yes > checking distutils?... yes > checking distutils works... yes > checking Numeric?... yes > checking Numarray?... > checking Python version string... 2.4 > checking install prefix for /usr/bin/python2.4... /usr > checking Prefix exists...... yes > checking for python include location... /usr/include/python2.4 > checking that include directory exists... yes > checking for python library location... /usr/lib/python2.4/site-package= s > checking that lib directory is accessable... yes > checking Python library... /usr/lib/python2.4 > checking site.py... /usr/lib/python2.4/site.py > checking site-packages... /usr/lib/python2.4/site-packages > checking for python lib/config location... /usr/lib/python2.4/config > checking that lib/config directory is accessable... yes > checking libpython2.4.a is there... yes > checking configuration Makefile is there... yes > checking module configuration table is there... yes > checking original Python there... yes > checking for --with-includes... no > checking for compiler based include directory... no > checking MPI_COMPILE_FLAGS... no > checking MPI_LD_FLAGS... no > 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 mpi.h usability... yes > checking mpi.h presence... yes > checking for mpi.h... yes > checking Python.h usability... yes > checking Python.h presence... yes > checking for Python.h... yes > checking Python CC... gcc -pthread > checking Python CFLAGS... -fno-strict-aliasing -DNDEBUG -O2 -g -pipe > -Wp,-D_FORTIFY_SOURCE=3D2 -fexceptions -m32 -march=3Di386 -mtune=3Dpent= ium4 > -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC > checking Python INCLUDEPY... /usr/include/python2.4 > checking Python OPT... -DNDEBUG -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=3D2 > -fexceptions -m32 -march=3Di386 -mtune=3Dpentium4 -fasynchronous-unwind= -tables > -D_GNU_SOURCE -fPIC > checking Python LDFLAGS... -L/usr/kerberos/lib > checking Python LINKFORSHARED... -Xlinker -export-dynamic > checking Python LDSHARED... gcc -pthread -shared > checking Python BLDSHARED... gcc -pthread -shared > checking Python LOCALMODLIBS... > checking Python BASEMODLIBS... > checking Python LIBS... -lpthread -ldl -lutil > checking Python LDLAST... > checking Python library options... -L/usr/lib/python2.4/config > -lpython2.4 -L/usr/kerberos/lib -Xlinker -export-dynamic -lpthread -l= dl > -lutil > checking for --with-dbfork... no > checking for --with-debug... no > checking python.exp file... no > checking sysconf(_SC_NPROCESSORS_CONF)... yes > checking for ANSI C header files... (cached) yes > checking local processor count for testing... 2 > checking for --with-libs... no > checking for pow in -lm... yes > checking for PyOS_StdioReadline... yes > checking for setlinebuf... yes > checking sys/param.h usability... yes > checking sys/param.h presence... yes > checking for sys/param.h... yes > checking Python links as is... yes > checking for MPI capability... yes > checking for Py_ReadOnlyBytecodeFlag... no > checking for MPI_Initialized()... yes > checking for MPI_Finalized()... yes > checking for MPI File operations (ROMIO)... yes > checking for AIX dynamic load... no > checking pm_util.h usability... no > checking pm_util.h presence... no > checking for pm_util.h... no > checking for mpc_flush... no > checking for mpc_isatty... no > checking for Electric Fence enabled?... no >=20 > I suspect that I am missing something (mpc_isatty?) and will poke aroun= d > to see what I need to do to get it. >=20 > -Doug >=20 >=20 >>I had this problem with pyMPI-2.0b0, at which point I was directed to u= se >>the CVS version, but the fix should be in b4. The other missing piece i= s >>the >>compile options, in that configure needs to be run: >> >>./configure --prefix=3D/usr --with-isatty >> >>Obviously --prefix=3D/usr depends on where the ultimate install will be= , >>but --with-isatty makes sure that the interactive console will work. Th= ere >>are some posts in November 2004 (see Julian cook, Mike Steder) that >>discuss >>a similar problem. There is another configure option with regard to >>Newlines, but normally that is not needed. Otherwise on Monday Pat Mill= er >>should be able to give better advice. >> >>Julian >=20 >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server.=20 > Download it for free - -and be entered to win a 42" plasma tv or your v= ery > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.p= hp > _______________________________________________ > Pympi-users mailing list > Pym...@li... > https://lists.sourceforge.net/lists/listinfo/pympi-users >=20 >=20 --=20 Douglas S. Blank, Assistant Professor db...@br..., (610)526-6501 Bryn Mawr College, Computer Science Program 101 North Merion Ave, Park Science Bld. Bryn Mawr, PA 19010 dangermouse.brynmawr.edu |
From: Pat M. <pat...@ll...> - 2005-09-26 21:56:10
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> I was able to compile pyMPI once I took out the offending lines, as you suggested below. > > I actually had something that worked between two particular machines for a short while, but I broke it again. I'm in the middle of upgrading the entire cluster, so I'll make sure that I have everything the same on all machines. > > There are so many places that can cause havoc: selinux, iptables, rsh, lam, mpirun, python... Does anyone have a step-by-step check list for getting up and running, especially on a Fedora Core 4 machine? I'll help write it, if I ever get it working... Doug, did you change int isatty(int filedes) __THROW { return (filedes == 0 || filedes == 1 || filedes == 2); } to int isatty(int filedes) { return (filedes == 0 || filedes == 1 || filedes == 2); } I should likely change it to something safer (if less readable) like: int isatty(int filedes) #ifdef __THROW __THROW #endif { return (filedes == 0 || filedes == 1 || filedes == 2); } The test suite (from make check which is more extensive than PyMPITest.py doesn't do a good job of testing interactive (and indeed, I diddn't build a version --with-isatty when I did the release test!). I'm not sure how to do that automatically. Pat -- Pat Miller | (925) 423-0309 | http://www.llnl.gov/CASC/people/pmiller I have discovered that all human evil comes from this, man's being unable to sit still in a room. -- Blaise Pascal, philosopher & mathematician (1623-1662) |
From: <db...@br...> - 2005-09-26 22:35:32
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Thanks! Now working. Details below. > Doug, > did you change > > int isatty(int filedes) __THROW { > return (filedes =3D=3D 0 || filedes =3D=3D 1 || filedes =3D=3D 2); > } > > to > > int isatty(int filedes) { > return (filedes =3D=3D 0 || filedes =3D=3D 1 || filedes =3D=3D 2); > } Originally, I had just deleted those lines. But I tried your safe version below and that gave an error in the make: pyMPI_isatty.c:43: Warning: FORMAT ERROR Traceback (most recent call last): File "./utils/grind_docs_and_prototypes.py", line 530, in ? actor.check(source,file) File "./utils/grind_docs_and_prototypes.py", line 179, in check method(kind,name,file,line,follow_line,*arguments) File "./utils/grind_docs_and_prototypes.py", line 306, in GLOBAL raise ValueError,follow ValueError: int isatty(int filedes) make[1]: *** [pyMPI_Externals.h] Error 1 make[1]: Leaving directory `/home/setup/pyMPI-2.4b3' make: *** [all] Error 2 Then I tried the version above without the __THROW, and that worked. Hope that gives you some hints on how you can write that portably. Thanks again, -Doug > I should likely change it to something safer (if less readable) like: > > > int isatty(int filedes) > #ifdef __THROW > __THROW > #endif > { > return (filedes =3D=3D 0 || filedes =3D=3D 1 || filedes =3D=3D 2); > } > > The test suite (from make check which is more extensive than PyMPITest.= py > doesn't do a good job of testing interactive (and indeed, I diddn't bui= ld > a version --with-isatty when I did the release test!). I'm not sure ho= w > to do that automatically. > > Pat > > |