[petsc-dev] Errors when testing PETSc build on Windows
Hector E Barrios Molano
hectorb at utexas.edu
Wed Jun 17 14:41:47 CDT 2015
Hi PETSc Experts!
I'm trying to build PETSc on a Windows machine, I got errors during
the test part. I downloaded petsc-dev from git.
This are my configuration command:
$ ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort'
--prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
--with-parmetis-include=/cygdrive/c/Installed/parmetis/include
--with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
--with-metis-include=/cygdrive/c/Installed/parmetis/include
--with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
--with-mpi-include=[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]
--with-mpi-lib=[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]
--with-blas-lapack-lib=[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]
--with-scalapack-include=/cygdrive/c/Installed/mkl/include
--with-scalapack-lib=[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]
--with-sowing=0
I was able con configure and compile:
make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
PETSC_ARCH=windows-intel all
However, when testing I got these errors:
$ make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
PETSC_ARCH=windows-intel test
Running test examples to verify correct installation
Using PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc and
PETSC_ARCH=windows-intel
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
lid velocity = 0.0016, prandtl # = 1, grashof # = 1
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] VecNorm_Seq line 240
C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\seq\bvec2.c
[0]PETSC ERROR: [0] VecNorm line 228
C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
[0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 150
C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
[0]PETSC ERROR: [0] SNESSolve line 3847
C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
[0]PETSC ERROR: [0] main line 108
C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See
http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.
[0]PETSC ERROR: Petsc Development GIT revision: unknown GIT Date: unknown
[0]PETSC ERROR: ./ex19 on a windows-intel named HECTOR-PC by hector
Wed Jun 17 14:21:38 2015
[0]PETSC ERROR: Configure options --with-cc="win32fe cl"
--with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/
--PETSC_ARCH=windows-intel
--with-parmetis-include=/cygdrive/c/Installed/parmetis/include
--with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
--with-metis-include=/cygdrive/c/Installed/parmetis/include
--with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
--with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
--with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
--with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
--with-scalapack-include=/cygdrive/c/Installed/mkl/include
--with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
--with-sowing=0
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0
---- error analysis -----
[0] on hector-PC
./ex19 aborted the job. abort code 59
---- error analysis -----
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2
MPI processes
See http://www.mcs.anl.gov/petsc/documentation/faq.html
lid velocity = 0.0016, prandtl # = 1, grashof # = 1
[0]PETSC ERROR:
[1]PETSC ERROR:
------------------------------------------------------------------------
------------------------------------------------------------------------
[0]PETSC ERROR:
[1]PETSC ERROR:
Caught signal number 11 SEGV: Segmentation Violation, probably memory
access out of range
Caught signal number 11 SEGV: Segmentation Violation, probably memory
access out of range
[0]PETSC ERROR:
[1]PETSC ERROR:
Try option -start_in_debugger or -on_error_attach_debugger
Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR:
[1]PETSC ERROR:
or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR:
[1]PETSC ERROR:
or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
memory corruption errors
or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
memory corruption errors
[0]PETSC ERROR:
[1]PETSC ERROR:
likely location of problem given in stack below
likely location of problem given in stack below
[0]PETSC ERROR:
[1]PETSC ERROR:
--------------------- Stack Frames ------------------------------------
--------------------- Stack Frames ------------------------------------
[0]PETSC ERROR:
[1]PETSC ERROR:
Note: The EXACT line numbers in the stack are not available,
Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:
[1]PETSC ERROR:
INSTEAD the line number of the start of the function
INSTEAD the line number of the start of the function
[0]PETSC ERROR:
[1]PETSC ERROR:
is given.
is given.
[0]PETSC ERROR:
[1]PETSC ERROR:
[0] VecNorm_MPI line 57 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\mpi\pvec2.c
[1] VecNorm_MPI line 57 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\impls\mpi\pvec2.c
[0]PETSC ERROR:
[1]PETSC ERROR:
[0] VecNorm line 228 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
[1] VecNorm line 228 C:\INSTAL~1\PETSC-~1\petsc\src\vec\vec\INTERF~1\rvector.c
[0]PETSC ERROR:
[1]PETSC ERROR:
[0] SNESSolve_NEWTONLS line 150
C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
[1] SNESSolve_NEWTONLS line 150
C:\INSTAL~1\PETSC-~1\petsc\src\snes\impls\ls\ls.c
[0]PETSC ERROR:
[1]PETSC ERROR:
[0] SNESSolve line 3847 C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
[1] SNESSolve line 3847 C:\INSTAL~1\PETSC-~1\petsc\src\snes\INTERF~1\snes.c
[0]PETSC ERROR:
[1]PETSC ERROR:
[0] main line 108 C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
[1] main line 108 C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex19.c
[0]PETSC ERROR:
[1]PETSC ERROR:
--------------------- Error Message
--------------------------------------------------------------
--------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR:
[1]PETSC ERROR:
Signal received
Signal received
[0]PETSC ERROR:
[1]PETSC ERROR:
See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR:
[1]PETSC ERROR:
Petsc Development GIT revision: unknown GIT Date: unknown
Petsc Development GIT revision: unknown GIT Date: unknown
[0]PETSC ERROR:
[1]PETSC ERROR:
./ex19 on a windows-intel named HECTOR-PC by hector Wed Jun 17 14:21:38 2015
./ex19 on a windows-intel named HECTOR-PC by hector Wed Jun 17 14:21:38 2015
[0]PETSC ERROR:
[1]PETSC ERROR:
Configure options --with-cc="win32fe cl" --with-fc="win32fe ifort"
--prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
--with-parmetis-include=/cygdrive/c/Installed/parmetis/include
--with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
--with-metis-include=/cygdrive/c/Installed/parmetis/include
--with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
--with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
--with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
--with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
--with-scalapack-include=/cygdrive/c/Installed/mkl/include
--with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
--with-sowing=0
Configure options --with-cc="win32fe cl" --with-fc="win32fe ifort"
--prefix=/cygdrive/c/Installed/petsc/ --PETSC_ARCH=windows-intel
--with-parmetis-include=/cygdrive/c/Installed/parmetis/include
--with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib
--with-metis-include=/cygdrive/c/Installed/parmetis/include
--with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib
--with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]"
--with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]"
--with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]"
--with-scalapack-include=/cygdrive/c/Installed/mkl/include
--with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib]"
--with-sowing=0
[0]PETSC ERROR:
[1]PETSC ERROR:
#1 User provided function() line 0 in unknown file
#1 User provided function() line 0 in unknown file
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0
[1] application aborted
aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 1
---- error analysis -----
[0-1] on hector-PC
./ex19 aborted the job. abort code 59
---- error analysis -----
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/cygdrive/c/Installed/petsc-dev/petsc/src/snes/examples/tutorials ex5f
*********************************************************
/cygdrive/c/Installed/petsc-dev/petsc/bin/win32fe/win32fe ifort -c
-MT -Z7 -fpp -I/cygdrive/c/Installed/petsc-dev/petsc/include
-I/cygdrive/c/Installed/petsc-dev/petsc/windows-intel/include
-I/cygdrive/c/Installed/parmetis/include
-I/cygdrive/c/Installed/msmpi/Include
-I/cygdrive/c/Installed/msmpi/Include/x64 -o ex5f.o ex5f.F
/cygdrive/c/Installed/petsc-dev/petsc/bin/win32fe/win32fe ifort -MT
-Z7 -fpp -o ex5f ex5f.o
-L/cygdrive/c/Installed/petsc-dev/petsc/windows-intel/lib -lpetsc
/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_ilp64.lib
/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_ilp64.lib
/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_ilp64.lib
/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib
/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib
/cygdrive/c/Installed/parmetis/lib/parmetis.lib
/cygdrive/c/Installed/parmetis/lib/metis.lib
/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib
/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib Gdi32.lib User32.lib
Advapi32.lib Kernel32.lib Ws2_32.lib
ex5f.obj : error LNK2019: unresolved external symbol SNESCREATE
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol
DMCREATEGLOBALVECTOR referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol VECDUPLICATE
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol DMDAGETCORNERS
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol
DMDAGETGHOSTCORNERS referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol SNESSETDM
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol
SNESSETFROMOPTIONS referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol
SNESGETITERATIONNUMBER referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol VECDESTROY
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol SNESDESTROY
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol DMDESTROY
referenced in function MAIN__
ex5f.obj : error LNK2019: unresolved external symbol MATSETVALUESLOCAL
referenced in function FORMJACOBIANLOCAL
ex5f.obj : error LNK2019: unresolved external symbol MATASSEMBLYBEGIN
referenced in function FORMJACOBIANLOCAL
ex5f.obj : error LNK2019: unresolved external symbol MATASSEMBLYEND
referenced in function FORMJACOBIANLOCAL
C:\INSTAL~1\PETSC-~1\petsc\src\snes\examples\TUTORI~1\ex5f.exe : fatal
error LNK1120: 14 unresolved externals
makefile:50: recipe for target 'ex5f' failed
make[3]: [ex5f] Error 96 (ignored)
/usr/bin/rm -f ex5f.o
Completed test examples
=========================================
Now to evaluate the computer systems you plan use - do:
make PETSC_DIR=/cygdrive/c/Installed/petsc-dev/petsc
PETSC_ARCH=windows-intel streams NPMAX=<number of MPI processes you
intend to use>
Best Regards,
Hector
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