Error: Can't open included file 'mpif.h'

[Justin Li]

Hi, 

I've just got the latest code from the website http://pencil-code.nordita.org/. The code is quite versatile and I am truly grateful for you guys' work. However, I encountered an error when I ran the samples with parallel computing, e.g. conv-slab, interstellar etc. The error is :

mpicomm.f90:55: Error: Can't open included file 'mpif.h'

But I do have openmpi installed on my system. When I run "mpif90 --show", the result is:

mpif90 --show

gfortran -I/usr/lib/openmpi/include -pthread -I/usr/lib/openmpi/lib -L/usr//lib -L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f

77 -lmpi -ldl -lhwloc

I've tried adding the path to Makefile by changing FFLAGS variable, but it didn't work. Besides, I copied "mpif.h" from that directory into "src/" but some new errors popped up.

I'm running pencil code on bash on Ubuntu on Windows. I've tried using my teacher's server. Same error was shown. :(

Could someone help me solve this? Thanks in advance :)

Cheers,

Justin

[Axel Brandenburg]

Hi Justin,
Not sure what is wrong there. By the way,
the latest version you would always get from

https://github.com/pencil-code

e.g. via

svn checkout https://github.com/pencil-code/pencil-code/trunk/ pencil-code

Is that what you did/meant?
Axel

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[Philippe-A. Bourdin]

Hello Justin Li,

would you please follow our "Quick start guide" that you find on our website under "Documentation"? In case the error persists, the guide also tells you what information we need in order to help you.

In advance, may I guess you use "ubuntu 16.04 LTS" together with the latest "OpenMPI"? I have recently seen that these versions together would NOT compile with our current default compiler settings, which insists on using the Fortran95 standard! If that is the case for you, we will have to find a solution...

Thanks and best greetings,
Philippe.

[Justin Li]

Hi Axel,

Yes I got the code from GitHub via git clone.

Best,

Justin

在 2016年12月8日星期四 UTC+8下午6:19:17，Axel写道：

[Justin Li]

Hi Philippe,

As you can see, I'm a beginner here, not so familiar with the compiler stuff. Here are the detailed information,

My linux version is "Ubuntu 14.04.5 LTS".

$ source sourceme.sh

PENCIL_HOME = </home/Pegacorn/pencil-code>

Adding /home/Pegacorn/pencil-code/{bin,utils{,/axel},remesh/bin} to PATH

$ echo $PENCIL_HOME/bin

/home/Pegacorn/pencil-code/bin

$ ls -la $PENCIL_HOME/bin

total 786

drwxrwxrwx 2 Pegacorn Pegacorn     0 Dec  9 13:12 .

drwxrwxrwx 2 Pegacorn Pegacorn     0 Dec  9 13:50 ..

-rwxrwxrwx 1 Pegacorn Pegacorn 53538 Dec  9 13:12 auto-test

-rwxrwxrwx 1 Pegacorn Pegacorn  2648 Dec  9 13:12 build-testcase-cvs

-rwxrwxrwx 1 Pegacorn Pegacorn  7285 Dec  9 13:12 copy-snapshots

-rwxrwxrwx 1 Pegacorn Pegacorn  6498 Dec  9 13:12 copy-snapshots_exp

-rwxrwxrwx 1 Pegacorn Pegacorn  1268 Dec  9 13:12 cvs-add-rundir

-rwxrwxrwx 1 Pegacorn Pegacorn  2537 Dec  9 13:12 cvsci_run

-rwxrwxrwx 1 Pegacorn Pegacorn  2332 Dec  9 13:12 cvsci_run_bash

-rwxrwxrwx 1 Pegacorn Pegacorn   392 Dec  9 13:12 dx_get_datadir

-rwxrwxrwx 1 Pegacorn Pegacorn   715 Dec  9 13:12 dx_list_varfiles

-rwxrwxrwx 1 Pegacorn Pegacorn   408 Dec  9 13:12 dx_table2csv

-rwxrwxrwx 1 Pegacorn Pegacorn   586 Dec  9 13:12 dx_var.general

-rw-rw-rw- 1 Pegacorn Pegacorn 71080 Dec  9 13:12 getconf.csh

lrwxrwxrwx 1 Pegacorn Pegacorn     6 Dec  9 13:12 git-pc -> pc_git

-rwxrwxrwx 1 Pegacorn Pegacorn  6565 Dec  9 13:12 gpgrowth

-rwxrwxrwx 1 Pegacorn Pegacorn  4165 Dec  9 13:12 mass-changer.pl

-rwxrwxrwx 1 Pegacorn Pegacorn  5304 Dec  9 13:12 mkdotin

-rwxrwxrwx 1 Pegacorn Pegacorn   580 Dec  9 13:12 mkinpars

-rwxrwxrwx 1 Pegacorn Pegacorn   476 Dec  9 13:12 mkproc-tree

-rwxrwxrwx 1 Pegacorn Pegacorn  1187 Dec  9 13:12 mkwww

-rwxrwxrwx 1 Pegacorn Pegacorn  1239 Dec  9 13:12 move-slice

-rwxrwxrwx 1 Pegacorn Pegacorn  6190 Dec  9 13:12 nl2idl

-rwxrwxrwx 1 Pegacorn Pegacorn  4708 Dec  9 13:12 nl2python

-rwxrwxrwx 1 Pegacorn Pegacorn  2703 Dec  9 13:12 pc_about

-rwxrwxrwx 1 Pegacorn Pegacorn  4296 Dec  9 13:12 pc_autocorrect_config

-rwxrwxrwx 1 Pegacorn Pegacorn 62205 Dec  9 13:12 pc_auto-test

-rwxrwxrwx 1 Pegacorn Pegacorn 12137 Dec  9 13:12 pc_build

-rwxrwxrwx 1 Pegacorn Pegacorn   643 Dec  9 13:12 pc_check_dir

-rwxrwxrwx 1 Pegacorn Pegacorn  1221 Dec  9 13:12 pc_check_revision

-rwxrwxrwx 1 Pegacorn Pegacorn  1630 Dec  9 13:12 pc_cleansrc

-rwxrwxrwx 1 Pegacorn Pegacorn 42573 Dec  9 13:12 pc_codingstyle

-rwxrwxrwx 1 Pegacorn Pegacorn   753 Dec  9 13:12 pc_collect_all

-rw-rw-rw- 1 Pegacorn Pegacorn 13139 Dec  9 13:12 pc_config.sh

-rwxrwxrwx 1 Pegacorn Pegacorn   811 Dec  9 13:12 pc_configtest

-rwxrwxrwx 1 Pegacorn Pegacorn  3838 Dec  9 13:12 pc_copyvar

-rwxrwxrwx 1 Pegacorn Pegacorn  3152 Dec  9 13:12 pc_cvsup

-rwxrwxrwx 1 Pegacorn Pegacorn  6098 Dec  9 13:12 pc_debug

-rwxrwxrwx 1 Pegacorn Pegacorn   767 Dec  9 13:12 pc_deprecated_slice_links

-rwxrwxrwx 1 Pegacorn Pegacorn  1485 Dec  9 13:12 pc_diffruns

-rwxrwxrwx 1 Pegacorn Pegacorn  5740 Dec  9 13:12 pc_dump_config

-rwxrwxrwx 1 Pegacorn Pegacorn  1741 Dec  9 13:12 pc_findconfig

-rwxrwxrwx 1 Pegacorn Pegacorn  8362 Dec  9 13:12 pc_fix_svn_properties

-rw-rw-rw- 1 Pegacorn Pegacorn 28180 Dec  9 13:12 pc_functions.sh

-rwxrwxrwx 1 Pegacorn Pegacorn  2184 Dec  9 13:12 pc_get_param_state

-rwxrwxrwx 1 Pegacorn Pegacorn 25788 Dec  9 13:12 pc_git

-rwxrwxrwx 1 Pegacorn Pegacorn   475 Dec  9 13:12 pc_grep

-rwxrwxrwx 1 Pegacorn Pegacorn   531 Dec  9 13:12 pc_inspectrun

-rwxrwxrwx 1 Pegacorn Pegacorn  2266 Dec  9 13:12 pc_jobtransfer

-rwxrwxrwx 1 Pegacorn Pegacorn  3766 Dec  9 13:12 pc_llsub

-rwxrwxrwx 1 Pegacorn Pegacorn  1379 Dec  9 13:12 pc_localize

-rwxrwxrwx 1 Pegacorn Pegacorn  9445 Dec  9 13:12 pc_mkdatadir

-rwxrwxrwx 1 Pegacorn Pegacorn   416 Dec  9 13:12 pc_mkproctree

-rwxrwxrwx 1 Pegacorn Pegacorn  4616 Dec  9 13:12 pc_newrun

-rwxrwxrwx 1 Pegacorn Pegacorn   202 Dec  9 13:12 pc_news

-rwxrwxrwx 1 Pegacorn Pegacorn  1027 Dec  9 13:12 pc_nowarn_to_kcq

-rwxrwxrwx 1 Pegacorn Pegacorn  2945 Dec  9 13:12 pc_pencil_swap

-rwxrwxrwx 1 Pegacorn Pegacorn    69 Dec  9 13:12 pc_phonelist

-rwxrwxrwx 1 Pegacorn Pegacorn  1793 Dec  9 13:12 pc_piechart

-rwxrwxrwx 1 Pegacorn Pegacorn   665 Dec  9 13:12 pc_qsub

-rwxrwxrwx 1 Pegacorn Pegacorn   575 Dec  9 13:12 pc_reduce_all

-rwxrwxrwx 1 Pegacorn Pegacorn  1471 Dec  9 13:12 pc_rename

-rwxrwxrwx 1 Pegacorn Pegacorn 51463 Dec  9 13:12 pc_run

-rwxrwxrwx 1 Pegacorn Pegacorn  5101 Dec  9 13:12 pc_script_test

-rwxrwxrwx 1 Pegacorn Pegacorn 13427 Dec  9 13:12 pc_setupsrc

-rwxrwxrwx 1 Pegacorn Pegacorn   235 Dec  9 13:12 pc_start

-rwxrwxrwx 1 Pegacorn Pegacorn  1538 Dec  9 13:12 pc_svn_add_rundir

-rwxrwxrwx 1 Pegacorn Pegacorn   349 Dec  9 13:12 pc_svnstatus_ignlinks

-rwxrwxrwx 1 Pegacorn Pegacorn  1473 Dec  9 13:12 pc_svnup

-rwxrwxrwx 1 Pegacorn Pegacorn  3547 Dec  9 13:12 pc_tsnap

-rwxrwxrwx 1 Pegacorn Pegacorn   319 Dec  9 13:12 pc_update_autotest.sh

-rwxrwxrwx 1 Pegacorn Pegacorn   581 Dec  9 13:12 pc_update_validated.sh

-rwxrwxrwx 1 Pegacorn Pegacorn  2069 Dec  9 13:12 pc_upgraderun

-rwxrwxrwx 1 Pegacorn Pegacorn   495 Dec  9 13:12 pc_useutil

-rwxrwxrwx 1 Pegacorn Pegacorn   755 Dec  9 13:12 pc_videofiles

-rwxrwxrwx 1 Pegacorn Pegacorn  1843 Dec  9 13:12 pc_worldmap

-rwxrwxrwx 1 Pegacorn Pegacorn  6018 Dec  9 13:12 pc_xmlexport

-rwxrwxrwx 1 Pegacorn Pegacorn 25109 Dec  9 13:12 pencil-test

-rw-rw-rw- 1 Pegacorn Pegacorn  3778 Dec  9 13:12 README

-rwxrwxrwx 1 Pegacorn Pegacorn   396 Dec  9 13:12 read_videofiles.csh

-rwxrwxrwx 1 Pegacorn Pegacorn 17634 Dec  9 13:12 reaper

-rwxrwxrwx 1 Pegacorn Pegacorn   367 Dec  9 13:12 reload

-rwxrwxrwx 1 Pegacorn Pegacorn  1190 Dec  9 13:12 remote-top

-rwxrwxrwx 1 Pegacorn Pegacorn  1111 Dec  9 13:12 restart-new-dir

-rwxrwxrwx 1 Pegacorn Pegacorn  1075 Dec  9 13:12 restart-new-dir-VAR

-rwxrwxrwx 1 Pegacorn Pegacorn 10234 Dec  9 13:12 run.csh

-rwxrwxrwx 1 Pegacorn Pegacorn   241 Dec  9 13:12 scpdatadir

-rwxrwxrwx 1 Pegacorn Pegacorn  1269 Dec  9 13:12 scp-proc-to-proc

-rwxrwxrwx 1 Pegacorn Pegacorn    61 Dec  9 13:12 setup-src

-rwxrwxrwx 1 Pegacorn Pegacorn  6248 Dec  9 13:12 start.csh

-rwxrwxrwx 1 Pegacorn Pegacorn 15039 Dec  9 13:12 start_run.csh

-rwxrwxrwx 1 Pegacorn Pegacorn  6498 Dec  9 13:12 summarize-history

drwxrwxrwx 2 Pegacorn Pegacorn     0 Dec  9 13:12 test

-rwxrwxrwx 1 Pegacorn Pegacorn    18 Dec  9 13:12 timestr

~/pencil-code/samples/conv-slab$ gcc --version

gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Copyright (C) 2013 Free Software Foundation, Inc.

~/pencil-code/samples/conv-slab$ gfortran --version

GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Copyright (C) 2013 Free Software Foundation, Inc.

Pegacorn@EXCALIBUR:~/pencil-code/samples/conv-slab$ pc_build --cleanall

Found config file </home/Pegacorn/pencil-code/config/os/GNU_Linux.conf>

Files will be linked to the root code directory '/home/Pegacorn/pencil-code'.

Linking job submission/execution scripts.

Linked root Makefile.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src'.

No such file: /home/Pegacorn/pencil-code/src/Makefile.machine

No such file: /home/Pegacorn/pencil-code/src/.cvsignore

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/special'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/pre_and_post_processing'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/magnetic'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/test_methods'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/inactive'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/experimental'.

Linking files in '/home/Pegacorn/pencil-code/samples/conv-slab/src/initial_condition'.

Rebuilding Makefile from Makefile.src.

(cd src; make FROM_PARENT=src/ -f Makefile.src cleann)

make[1]: Entering directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

rm -f *.x *.o *.a *.mod *.d cparam*.inc cparam_pencils*.inc *.il

rm -f special/*.o special/*.mod

rm -f initial_condition/*.o initial_condition/*.mod

rm -f experimental/*.o experimental/*.mod

rm -f pre_and_post_processing/*.o pre_and_post_processing/*.x

rm -f .current-precision

rm -f *.dot *.ps  # Dependency diagram files

rm -f work.pc work.pcl .build*

printf "# %s\n" "Empty" "(This file was written by 'make')" > Makefile.inc

printf "# %s\n" "Empty" "(This file was written by 'make')" > Makefile-standard.inc

rm -f Makefile src/Makefile Makefile_inc TAGS  *mpicomm_.f90 mpicomm_double*.f90

rm -rf semiauto-conf_tmp f90_qnd_log_dir

rm -f *.inc && touch Makefile.inc Makefile-standard.inc

make  -f Makefile.src Makefile

make[2]: Entering directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

scripts/check-mkfile Makefile.local Makefile.src

env ADAPT_MKFILE= scripts/adapt-mkfile Makefile.src Makefile

make[2]: Leaving directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

make[1]: Leaving directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

Pegacorn@EXCALIBUR:~/pencil-code/samples/conv-slab$ pc_build -d

          'Makefile' => [

                          'MAKE_VAR1 = -j',

                          'FFLAGS_DOUBLE = -r8',

                          'CFLAGS_DOUBLE = -DDOUBLE_PRECISION',

                          'LD_MPI =',

                          'CFLAGS_FFTW3 =',

                          'FFLAGS_FFTW3 =',

                          'LD_FFTW3 =',

                          'CFLAGS_FFTW2 =',

                          'FFLAGS_FFTW2 =',

                          'LD_FFTW2 =',

                          'FC = gfortran',

                          'F77 = $(FC)',

                          'FFLAGS += -O',

                          'FFLAGS_DOUBLE = -fdefault-real-8 -fdefault-double-8',

                          'FSTD_95 = -std=f95',

                          'FSTD_2003 = -std=f2003',

                          'CC = gcc',

                          'CFLAGS = -DFUNDERSC=1',

                          'CFLAGS_DOUBLE = -DDOUBLE_PRECISION'

                        ]

        };

Running make '-j' 'FFLAGS_DOUBLE=-fdefault-real-8 -fdefault-double-8' 'CFLAGS_DOUBLE=-DDOUBLE_PRECISION' 'LD_MPI=' 'CFLAGS_FFTW3=' 'FFLAGS_FFTW3=' 'LD_FFTW3=' 'CFLAGS_FFTW2=' 'FFLAGS_FFTW2=' 'LD_FFTW2=' 'FC=gfortran' 'F77=$(FC)

' 'FFLAGS=-O' 'FSTD_95=-std=f95' 'FSTD_2003=-std=f2003' 'CC=gcc' 'CFLAGS=-DFUNDERSC=1' 'default_to_be'

MAKING src/Makefile.inc

touch src/.build-history

echo Pegacorn"@"`hostname` "("`date`")" >> src/.build-history

( cd src && \

          echo "===== " make FROM_PARENT=src/ -f Makefile.src code "====="; \

          make FROM_PARENT=src/ -f Makefile.src default_to_be \

        )

=====  make FROM_PARENT=src/ -f Makefile.src code =====

make[1]: Entering directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

${PENCIL_HOME}/utils/pc_identify_revision --reset

make -f Makefile.src  start.o run.o combine_videofiles.o read_videofiles.o read_all_videofiles.o read_vectorfiles.o pre_and_post_processing/pc_collect.o pre_and_post_processing/pc_reduce.o pre_and_post_processing/pc_distribute.

o pre_and_post_processing/pc_distribute_z.o pre_and_post_processing/pc_extract.o pre_and_post_processing/pc_configtest.o pre_and_post_processing/pc_tecplot.o pre_and_post_processing/pc_tecplot_solid.o start.x run.x combine_vide

ofiles.x read_videofiles.x read_all_videofiles.x read_vectorfiles.x pre_and_post_processing/pc_collect.x pre_and_post_processing/pc_reduce.x pre_and_post_processing/pc_distribute.x pre_and_post_processing/pc_distribute_z.x pre_

and_post_processing/pc_extract.x pre_and_post_processing/pc_configtest.x pre_and_post_processing/pc_tecplot.x pre_and_post_processing/pc_tecplot_solid.x

make[2]: Entering directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

gfortran -O     -std=f95 -o mpicomm.o -c mpicomm.f90

make[2]: `combine_videofiles.o' is up to date.

make[2]: `read_videofiles.o' is up to date.

make[2]: `read_all_videofiles.o' is up to date.

make[2]: `read_vectorfiles.o' is up to date.

make[2]: `combine_videofiles.x' is up to date.

make[2]: `read_videofiles.x' is up to date.

make[2]: `read_all_videofiles.x' is up to date.

make[2]: `read_vectorfiles.x' is up to date.

mpicomm.f90:55: Error: Can't open included file 'mpif.h'

make[2]: *** [mpicomm.o] Error 1

make[2]: Leaving directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

make[1]: *** [code] Error 2

make[1]: *** Waiting for unfinished jobs....

make[1]: Leaving directory `/home/Pegacorn/pencil-code/samples/conv-slab/src'

make: *** [default_to_be] Error 2

'make -j FFLAGS_DOUBLE=-fdefault-real-8 -fdefault-double-8 CFLAGS_DOUBLE=-DDOUBLE_PRECISION LD_MPI= CFLAGS_FFTW3= FFLAGS_FFTW3= LD_FFTW3= CFLAGS_FFTW2= FFLAGS_FFTW2= LD_FFTW2= FC=gfortran F77=$(FC) FFLAGS=-O FSTD_95=-std=f95 FS

TD_2003=-std=f2003 CC=gcc CFLAGS=-DFUNDERSC=1 default_to_be' failed: <>

Pegacorn@EXCALIBUR:~/pencil-code/samples/conv-slab$ mpicc --version

gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Copyright (C) 2013 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Pegacorn@EXCALIBUR:~/pencil-code/samples/conv-slab$ mpif90 --version

GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Copyright (C) 2013 Free Software Foundation, Inc.

Pegacorn@EXCALIBUR:~/pencil-code/samples/conv-slab$ mpiexec --version

HYDRA build details:

    Version:                                 3.0.4

    Release Date:                            Wed Apr 24 10:08:10 CDT 2013

    CC:                              cc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro

    CXX:                             c++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro

    F77:                             gfortran -g -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro

    F90:                             gfortran  -Wl,-Bsymbolic-functions -Wl,-z,relro

    Configure options:                       '--disable-option-checking' '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=

/etc' '--localstatedir=/var' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--libexecdir=${prefix}/lib/x86_64-linux-gnu' '--disable-maintainer-mode' '--disable-dependency-tracking' '--enable-shared' '--enable-fc' '--disable-rpath'

'--disable-wrapper-rpath' '--sysconfdir=/etc/mpich' '--libdir=/usr/lib/x86_64-linux-gnu' '--includedir=/usr/include/mpich' '--docdir=/usr/share/doc/mpich' '--with-hwloc-prefix=system' '--enable-checkpointing' '--with-hydra-ckpo

intlib=blcr' 'build_alias=x86_64-linux-gnu' 'MPICHLIB_CFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security' 'MPICHLIB_CXXFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -W

error=format-security' 'MPICHLIB_FFLAGS=-g -O2' 'MPICHLIB_FCFLAGS=-g -O2' 'CFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -

Werror=format-security -O2' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro ' 'CPPFLAGS=-D_FORTIFY_SOURCE=2 -I/build/buildd/mpich-3.0.4/src/mpl/include -I/build/buildd/mpich-3.0.4/src/mpl/include -I/build/buildd/mpich-3.0.4/src/

openpa/src -I/build/buildd/mpich-3.0.4/src/openpa/src -I/build/buildd/mpich-3.0.4/src/mpi/romio/include' 'CXXFLAGS=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --p

aram=ssp-buffer-size=4 -Wformat -Werror=format-security -O2' 'F77=gfortran' 'FFLAGS=-g -O2 -g -O2 -O2' 'FC=gfortran' '--cache-file=/dev/null' '--srcdir=.' 'CC=cc' 'LIBS=-lrt -lcr -lpthread '

    Process Manager:                         pmi

    Launchers available:                     ssh rsh fork slurm ll lsf sge manual persist

    Topology libraries available:            hwloc

    Resource management kernels available:   user slurm ll lsf sge pbs cobalt

    Checkpointing libraries available:       blcr

    Demux engines available:                 poll select

Thank you sooo much for your help. :)

Best regards,

Justin 

[Philippe-A. Bourdin]

Hello Justin Li,

from the version you use, your installation looks good to me.
Because you like to use MPI, use need at least this option for compilation:

pc_build -f GNU-GCC_MPI

This should work for you out-of-the-box.
You may also create a "host-configuration" file for your computer, which is explained in the quick start guide and also in the manual.

Thanks and best greetings,
Philippe Bourdin.

[Justin Li]

Hi Philippe,

Many thanks for your help! I've tried pc_build -f GNU-GCC_MPI. The compilation process looks good now. No error occured. However, when I proceed to "pc_start", there are still some problems with MPI. I've tested conv-slab, interstellar, 2d-tests/Kelvin_ Helmholtz. interstellar is doing great, but conv-slab and Kelvin-Helmholtz gave me the same error after the "pc_start" command. Any ideas? Here are the outputs

double check that everything has shut down cleanly.

  Reason:     Before MPI_INIT completed

  Local host: EXCALIBUR

  PID:        7078

--------------------------------------------------------------------------

[EXCALIBUR:07079] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 231

[EXCALIBUR:07079] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 140

[EXCALIBUR:07079] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file runtime/orte_init.c at line 128

--------------------------------------------------------------------------

It looks like orte_init failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during orte_init; some of which are due to configuration or

environment problems.  This failure appears to be an internal failure;

here's some additional information (which may only be relevant to an

Open MPI developer):

  orte_ess_set_name failed

  --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS

--------------------------------------------------------------------------

--------------------------------------------------------------------------

It looks like MPI_INIT failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during MPI_INIT; some of which are due to configuration or environment

problems.  This failure appears to be an internal failure; here's some

additional information (which may only be relevant to an Open MPI

developer):

  ompi_mpi_init: orte_init failed

  --> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)

--------------------------------------------------------------------------

[EXCALIBUR:7079] *** An error occurred in MPI_Init

[EXCALIBUR:7079] *** on a NULL communicator

[EXCALIBUR:7079] *** Unknown error

[EXCALIBUR:7079] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort

--------------------------------------------------------------------------

An MPI process is aborting at a time when it cannot guarantee that all

of its peer processes in the job will be killed properly.  You should

double check that everything has shut down cleanly.

  Reason:     Before MPI_INIT completed

  Local host: EXCALIBUR

  PID:        7079

--------------------------------------------------------------------------

===================================================================================

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

=   EXIT CODE: 1

=   CLEANING UP REMAINING PROCESSES

=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

===================================================================================

Again, thank you very much! :)

Best regards,

Justin

[Justin Li]

Hi Philippe,

I think I've asked a dumb question. The problem is fixed. The reason I think is that I have mpich & openmpi on my system. It all works great now after I removed mpich. 

You guys are fantastic. I would like to express my most sincere gratitude and appreciation for your help! :)

Best regards,

Justin

On Friday, December 9, 2016 at 9:27:27 PM UTC+8, Philippe-A. Bourdin wrote: