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-   -   missing vtf3.h BPatch.h papi.h (http://www.cfd-online.com/Forums/openfoam-installation/80787-missing-vtf3-h-bpatch-h-papi-h.html)

linch October 6, 2010 10:46

missing vtf3.h BPatch.h papi.h
 
Hello OF-community,

trying to compile ThirdParty 1.7.1 I am expecting errors during the compilation of the openmpi-1.4.1. At the step "Configuring contributed software packages" it says:

Quote:

configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no BPatch.h found; check path for Dyninst package first...
configure: error: no papi.h found; check path for PAPI package first...
Using aptitude search on debian linux 2.6.32-5-amd64 I don't find theese packages. Does anybody know, where to get the mentioned files and where to place them?

Regards,

wyldckat October 7, 2010 07:32

Greetings Illya,

I know I've had this problem before, but I'm not 100% certain how I fixed it...

But how exactly are you building OpenMPI? Manually or using the Allwmake script in the ThirdParty folder?

Additionally, if you are using Debian, then this list of packages should work for you too: Building OpenFOAM1.7.0 from source post #4 and onward

Best regards,
Bruno

linch October 7, 2010 08:14

Hi Bruno,

thanks for the reply. Because of being newbie in OpenFOAM as well as in linux I use the Allwmake script.

There are quite a lot of packages listed in the thread. I hope that installing them will cure the problems.

EDIT: since I have no administrator rights, I can not install the packages by myself. And the admin refuses to install the whole bunch of packages until I exactly know which of them I do really need. So the question remains open.

wyldckat October 7, 2010 18:01

Hi Illya,
Quote:

Originally Posted by linch (Post 278270)
EDIT: since I have no administrator rights, I can not install the packages by myself. And the admin refuses to install the whole bunch of packages until I exactly know which of them I do really need. So the question remains open.

Well, I can't remember by heart which one was it :( And I can't find those headers in my Ubuntu system either, so I can only assume that OpenMPI's configure script can deduce that there are better options than those specific headers/packages, once those options are available.
But this weekend I'll try to get some time to figure out which one might it be.

But you could also request your system administrator to simply install the OpenMPI version available for your system. And if not OpenMPI, any other MPI should work too, just a matter of configuring the script "$WM_PROJECT_DIR/etc/settings.sh" to the desired MPI library.

Those packages listed on that link, also include the necessary packages for building ParaView, albeit some of them might be available for your system, since it's a bit old.

Best regards,
Bruno

wyldckat October 8, 2010 21:15

Hi Illya,

OK, I've tested in a virtual machine with Ubuntu 10.04 (which is based in Debian). The only packages that I needed for building OpenMPI were:
Code:

gcc g++ flex
By what I can figure out, what happens is this: even if a package is missing, OpenMPI will continue if possible. So, even if you got those three errors about VTF3, PAPI and BPatch, they aren't crucial since they are simply added value if available.
So, if you run this command:
Code:

ls -l $MPI_ARCH_PATH
You should see something like this:
Code:

drwxr-xr-x 7 user user 4096 2010-10-09 01:50 ./
drwxr-xr-x 3 user user 4096 2010-10-09 01:49 ../
drwxr-xr-x 2 user user 4096 2010-10-09 01:53 bin/
drwxr-xr-x 2 user user 4096 2010-10-09 01:51 etc/
drwxr-xr-x 3 user user 4096 2010-10-09 01:53 include/
drwxr-xr-x 3 user user 4096 2010-10-09 01:53 lib/
drwxr-xr-x 5 user user 4096 2010-10-09 01:53 share/

This should mean, in a clean build (i.e., started from scratch), that OpenMPI was in fact built successfully :)

Now, if the Allwmake came to an end with an error in the end, then something else went wrong. Other than that, you should be good to continue building!

Best regards,
Bruno

linch October 11, 2010 05:03

Hi Bruno,

with ls -l $MPI_ARCH_PATH I can see the folder you listed and everything seems to be ok insofar. Thank you!

maddalena September 26, 2011 08:24

everything is fine or not?
 
Hello Bruno,
I am trying to install OpenFOAM 2.0.1 on a Gnome Debian 2.22.3. I am also getting the following:
Code:

configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no BPatch.h found; check path for Dyninst package first...
configure: error: no f2c.h found; check path for CLAPACK package first...
configure: error: MPI Correctness Checking support cannot be built inside Open MPI
configure: error: no jvmti.h found; check path for JVMTI package first...
configure: error: no papi.h found; check path for PAPI package first...
configure: error: no libcpc.h found; check path for CPC package first...
configure: error: no ctool/ctool.h found; check path for CTool package first...

however, the installation continues without further complains. In addition, the ls -l $MPI_ARCH_PATH command gives exactly what you said above.
In conclusion, I should not worry about those errors, should I?

mad

wyldckat September 26, 2011 08:33

Hi Maddalena,

I vaguely remember seeing those errors and even with them everything else built properly, so I suppose so.
If:
  • It had stopped at the end of the "configure" step;
  • Or stopped during the build process, with an error related to one of the errors given during configure;
then yes, it would be a valid reason for concern! :)

Best regards,
Bruno

linch July 18, 2012 12:00

Hi Bruno,

me again 1.5 years later. I've got new pc with new Debian
Code:

(Linux version 2.6.32-5-amd64 (Debian 2.6.32-45) (dannf@debian.org) (gcc version 4.3.5 (Debian 4.3.5-4) ))
Trying to compile the OF 2.1.x I'm getting almost the same erros as last time:
Quote:

configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no BPatch.h found; check path for Dyninst package first...
configure: error: no f2c.h found; check path for CLAPACK package first...
configure: error: MPI Correctness Checking support cannot be built inside Open MPI
configure: error: no jvmti.h found; check path for JVMTI package first...
configure: error: no papi.h found; check path for PAPI package first...
configure: error: no libcpc.h found; check path for CPC package first...
configure: error: no ctool/ctool.h found; check path for CTool package first...
and additionally this one:
Quote:

config.status: executing libtool commands
+ make -j 4
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/shevchuk/OpenFOAM/ThirdParty-2.1.x/openmpi-1.5.3/config/missing --run aclocal-1.11 -I config
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
configure.ac:953: warning: OMPI_CONFIGURE_SETUP is m4_require'd but not m4_defun'd
config/ompi_mca.m4:37: OMPI_MCA is expanded from...
configure.ac:953: the top level
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/shevchuk/OpenFOAM/ThirdParty-2.1.x/openmpi-1.5.3/config/missing --run autoconf
cd . && /bin/bash /home/shevchuk/OpenFOAM/ThirdParty-2.1.x/openmpi-1.5.3/config/missing --run automake-1.11 --foreign
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
sh: config/ompi_get_version.sh: not found
configure.ac:953: warning: OMPI_CONFIGURE_SETUP is m4_require'd but not m4_defun'd
config/ompi_mca.m4:37: OMPI_MCA is expanded from...
configure.ac:953: the top level
configure.ac:695: error: possibly undefined macro: AC_CHECK_FUNC
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
make: *** [configure] Error 1
and at the end a couple of similar looking errors like:
Quote:

./configure: line 5147: syntax error near unexpected token `Loading'
./configure: line 5147: ` OMPI_LOG_MSG(Loading environment file $with_platform, with contents below)'
make: *** [config.status] Error 2
This time ls -l $MPI_ARCH_PATH isn't successful, what means that MPI wasn't compiled. Do you have any idea what the reason could be? Obviously I am missing some packages.

Best regards,
Ilya

wyldckat July 18, 2012 16:21

Hi Ilya,

I'll need more info about which Debian version you're using. Try this command:
Code:

cat /etc/lsb-release
I'll look into this tomorrow night. Any special details about the Debian installation? And/or if you're using a shell other than Bash or Dash?

Best regards,
Bruno

linch July 19, 2012 05:00

1 Attachment(s)
Hi Bruno,

there is no lsb-release in /etc But:
Code:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 6.0.5 (squeeze)
Release:        6.0.5
Codename:      squeeze


Here is the complete ThirdParty make log, if it helps.

Thanks a lot!
Ilya

linch July 19, 2012 07:29

What I have to add, there is openmpi already installed in /usr/local/mpich independently from OF. So of the ThirdParty-openmpi installations fails, it may be possible to link the "external" openmpi to OF. What do you think about it?

wyldckat July 20, 2012 05:28

Hi Ilya,

I'll try to replicate the installation on a virtual machine later today, with an up-to-date Debian 6 x86_64 (== amd64) installation.

As for MPICH:
  1. Is it MPICH or MPICH2?
  2. When you run:
    Code:

    which mpicc
    Is it the one from MPICH that appears or none appears?
  3. How was MPICH installed? From Debian or manually installed?
Why not configure your OpenFOAM installation to use that MPI toolbox instead of Open-MPI? You'll need to configure these files:
  1. "OpenFOAM-2.1.x/etc/bashrc" - change OPENMPI to MPICH
  2. "OpenFOAM-2.1.x/etc/config/settings.sh" - find the MPICH entry and reconfigure the parameters located in that block of code!
____
edit:
Well, I've just tested now on a VM with Debian 6 and it built things just fine.
I've got feeling that you have a machine setup that is influencing the results you and I are getting. The installed MPICH version you got may be only the tip of the iceberg :(

But like I've wrote above: maybe it's best that you use the MPICH library you already have. By the way, which version do you have? Because I tried getting the source code for the old MPICH1 for trying to replicate the installation and didn't find it after a 5min search :(

Ah, last but not least, try installing the Open-MPI version that Debian has (scotch as well):
Code:

sudo apt-get install libscotch-dev libopenmpi-dev
Then in OpenFOAM's "etc/bashrc", change "OPENMPI" to "SYSTEMOPENMPI".

____

Best regards,
Bruno

linch July 20, 2012 10:41

Hi Bruno,

a general question, what's the difference between opnmpi & mpich? Does it matter, which one to use?

1) I have no idea. How can I find it out? A little bit strange is the following: the mpich dir contains dirs
Quote:

bin etc include lib openmpi-1.5.3
and there is a lot of ompi called stuff in bin & etc dirs:
Quote:

/usr/local/mpich/etc$ ll
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpic++ -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpicc -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpiCC -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpicc-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpiCC-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpic++-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpicxx -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpicxx-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 7 18. Jul 13:13 mpiexec -> orterun*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpif77 -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpif77-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpif90 -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 mpif90-vt -> opal_wrapper*
lrwxrwxrwx 1 root staff 7 18. Jul 13:13 mpirun -> orterun*
lrwxrwxrwx 1 root staff 10 18. Jul 13:13 ompi-clean -> orte-clean*
-rwxr-xr-x 1 root staff 202531 18. Jul 13:13 ompi_info*
lrwxrwxrwx 1 root staff 8 18. Jul 13:13 ompi-iof -> orte-iof*
-rwxr-xr-x 1 root staff 61232 18. Jul 13:13 ompi-probe*
-rwxr-xr-x 1 root staff 84492 18. Jul 13:13 ompi-profiler*
lrwxrwxrwx 1 root staff 7 18. Jul 13:13 ompi-ps -> orte-ps*
-rwxr-xr-x 1 root staff 78551 18. Jul 13:13 ompi-server*
lrwxrwxrwx 1 root staff 8 18. Jul 13:13 ompi-top -> orte-top*
-rwxr-xr-x 1 root staff 89852 18. Jul 13:13 opal_wrapper*
-rwxr-xr-x 1 root staff 325542 18. Jul 13:13 opari*
-rwxr-xr-x 1 root staff 2370 18. Jul 13:13 orte-bootproxy.sh*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 ortec++ -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 ortecc -> opal_wrapper*
lrwxrwxrwx 1 root staff 12 18. Jul 13:13 orteCC -> opal_wrapper*
-rwxr-xr-x 1 root staff 70926 18. Jul 13:13 orte-clean*
-rwxr-xr-x 1 root staff 60268 18. Jul 13:13 orted*
-rwxr-xr-x 1 root staff 75277 18. Jul 13:13 orte-iof*
-rwxr-xr-x 1 root staff 82283 18. Jul 13:13 orte-ps*
-rwxr-xr-x 1 root staff 188663 18. Jul 13:13 orterun*
-rwxr-xr-x 1 root staff 108702 18. Jul 13:13 orte-top*
-rwxr-xr-x 1 root staff 4214 18. Jul 13:13 orte_wrapper_script*
-rwxr-xr-x 1 root staff 191659 18. Jul 13:13 otfaux*
-rwxr-xr-x 1 root staff 70942 18. Jul 13:13 otfcompress*
-rwxr-xr-x 1 root staff 57057 18. Jul 13:13 otfconfig*
lrwxrwxrwx 1 root staff 11 18. Jul 13:13 otfdecompress -> otfcompress*
-rwxr-xr-x 1 root staff 83706 18. Jul 13:13 otfdump*
-rwxr-xr-x 1 root staff 100363 18. Jul 13:13 otfinfo*
-rwxr-xr-x 1 root staff 108934 18. Jul 13:13 otfmerge*
-rwxr-xr-x 1 root staff 607083 18. Jul 13:13 otfprofile*
-rwxr-xr-x 1 root staff 104056 18. Jul 13:13 otfshrink*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtc++ -> vtwrapper*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtcc -> vtwrapper*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtCC -> vtwrapper*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtcxx -> vtwrapper*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtf77 -> vtwrapper*
lrwxrwxrwx 1 root staff 9 18. Jul 13:13 vtf90 -> vtwrapper*
-rwxr-xr-x 1 root staff 288245 18. Jul 13:13 vtfilter*
-rwxr-xr-x 1 root staff 412484 18. Jul 13:13 vtunify*
-rwxr-xr-x 1 root staff 426896 18. Jul 13:13 vtunify-mpi*
-rwxr-xr-x 1 root staff 166540 18. Jul 13:13 vtwrapper*
Quote:

/usr/local/mpich/etc$ ll
-rw-r--r-- 1 root staff 1508 18. Jul 13:13 openmpi-default-hostfile
-rw-r--r-- 1 root staff 2812 18. Jul 13:12 openmpi-mca-params.conf
-rw-r--r-- 1 root staff 1444 18. Jul 13:13 openmpi-totalview.tcl
-rw-r--r-- 1 root staff 83 18. Jul 13:13 vt-java-default-filter.spec
So may be it isn't mpich at all, but openmpi installed into the mpich dir.

2)
Quote:

$ which mpicc
/usr/bin/mpicc
3) I suppose it was installed manually

P.S. libscotch-dev libopenmpi-dev are already there, so I don't need to install them

wyldckat July 20, 2012 10:51

Hi Ilya,

I'm guessing that installing Open-MPI in those machines at your workplace can be a pain, which is why the administrator installs it manually.
The "mpich" folder must be a legacy thing, to keep things compatible with the workflow existent there.

I believe that version one of MPICH was created in a time when no other MPI was open-source. Open-MPI came to life as a need for a more generic and open MPI toolbox. But I guess that Wikipedia should know more than me :D :

And like I wrote before, the trick for your system should be:
Quote:

In OpenFOAM's "etc/bashrc", change "OPENMPI" to "SYSTEMOPENMPI".
Then run wmSET (or start a new terminal) and you can then go back to building OpenFOAM!

Best regards,
Bruno

linch July 20, 2012 11:01

Hi Bruno,

Quote:

Originally Posted by wyldckat (Post 372553)
Then in OpenFOAM's "etc/bashrc", change "OPENMPI" to "SYSTEMOPENMPI".

I made the change in the OF bashrc, but when I try to source it, I get the following error:
Quote:

Cannot open configuration file /home/shevchuk/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/mpicc-wrapper-data.txt
Error parsing data file mpicc: Not found
Best regards,
Ilya

wyldckat July 20, 2012 11:22

Mmm... you better start a new terminal, because the environment is already contaminated with the old option.

linch July 20, 2012 11:41

Hi Bruno,

I've started a new terminal and executed ./Allwmake script from the OpenFOAM-2.1.x dir. There were no errors this time. But if I try to start a parallel simulation a get a bunch of errors looking like this:
Quote:

[wmpc41:30869] [[47911,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/util/nidmap.c at line 371
[wmpc41:30869] [[47911,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
[wmpc41:30869] [[47911,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line 173
--------------------------------------------------------------------------
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_base_build_nidmap failed
--> Returned value Data unpack would read past end of buffer (-26) instead of ORTE_SUCCESS
should I recompile the complete OF build (wclean all bevor Allwmake)?

Best regards,
Ilya

wyldckat July 20, 2012 11:44

Hi Ilya,

This should be enough, without having to rebuild the whole OpenFOAM source:
Code:

src
cd Pstream
wclean all
wmake all

Best regards,
Bruno

linch July 20, 2012 11:54

1 Attachment(s)
Hi Bruno,

there are apparently no problems during the buid any more, but mpi still doesn't work properly. Here is an error log example.

Best,
Ilya


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