I couple of days ago I bought Parallels for my mac and then installed debian jessie. After installing some required packages today I am attempting to build ET-Hilbert. The build goes ok until the end when I get some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem with MPI. I have openmpi installed as suggested at the top of the debian.cfg file. I do not have any other mpi flavors installed.
Can someone please take a look at the attached file and let me know whether something sticks out?
Thanks very much.
Comer
Comer
It seems that Cactus doesn't realize that MPI requires a few additional libraries. Most likely, this list of additional libraries varies from system to system, and may depend on the Debian version. Usually, Cactus use shared libraries, and they contain enough information to automatically find and use all necessary dependencies. Apparently you are using static libraries (see "libmpi.a" in the beginning of the error messages), and this requires listing dependencies manually.
I also just see that Cactus build MPI by itself, which it shouldn't have if there is an existing MPI. Also, if Cactus builds MPI, it should have correctly figured out the dependencies! Maybe adding "MPI_DIR = /usr" to the debian.cfg option list would help.
Do you have the output that Cactus produces when configuring? This would tell us why Cactus didn't find Debian's MPI. You could build from scratch, saving all output, and attaching this to a bug report.
-erik
On Fri, Aug 7, 2015 at 1:07 PM, Comer Duncan comer.duncan@gmail.com wrote:
I couple of days ago I bought Parallels for my mac and then installed debian jessie. After installing some required packages today I am attempting to build ET-Hilbert. The build goes ok until the end when I get some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem with MPI. I have openmpi installed as suggested at the top of the debian.cfg file. I do not have any other mpi flavors installed.
Can someone please take a look at the attached file and let me know whether something sticks out?
Thanks very much.
Comer
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
On 7 Aug 2015, at 19:29, Erik Schnetter schnetter@cct.lsu.edu wrote:
Comer
It seems that Cactus doesn't realize that MPI requires a few additional libraries. Most likely, this list of additional libraries varies from system to system, and may depend on the Debian version. Usually, Cactus use shared libraries, and they contain enough information to automatically find and use all necessary dependencies. Apparently you are using static libraries (see "libmpi.a" in the beginning of the error messages), and this requires listing dependencies manually.
I also just see that Cactus build MPI by itself, which it shouldn't have if there is an existing MPI. Also, if Cactus builds MPI, it should have correctly figured out the dependencies! Maybe adding "MPI_DIR = /usr" to the debian.cfg option list would help.
Do you have the output that Cactus produces when configuring? This would tell us why Cactus didn't find Debian's MPI. You could build from scratch, saving all output, and attaching this to a bug report.
This happens a lot. It would be good to be able to put something into the optionlist which told the MPI thorn that it should use an auto-detected library, rather than building the library.
Hello all,
This happens a lot. It would be good to be able to put something into the optionlist which told the MPI thorn that it should use an auto-detected library, rather than building the library.
Most thorns support a XXX_DIR=NO_BUILD option which then (depends on the thorn) may require you to actually specify the location of the libraries or may still allow searching for it. Basically all auto-detection (with the exception of MPI which also seems to fail here) should fail on modern Debian/Ubuntu systems that support "multi-arch" installations since the libraries are no longer in /usr/lib but in /usr/lib/x86-amd64 or so. Bruno was working on fixing this before the last release but the results were too fragile to be included in the current release branch.
Yours, Roland
On 17 Aug 2015, at 08:21, Roland Haas rhaas@aei.mpg.de wrote:
Hello all,
This happens a lot. It would be good to be able to put something into the optionlist which told the MPI thorn that it should use an auto-detected library, rather than building the library.
Most thorns support a XXX_DIR=NO_BUILD option which then (depends on the thorn) may require you to actually specify the location of the libraries or may still allow searching for it. Basically all auto-detection (with the exception of MPI which also seems to fail here) should fail on modern Debian/Ubuntu systems that support "multi-arch" installations since the libraries are no longer in /usr/lib but in /usr/lib/x86-amd64 or so. Bruno was working on fixing this before the last release but the results were too fragile to be included in the current release branch.
I know about the NO_BUILD option, but was under the impression that it doesn't do or mean what it appears to mean. I can't find any evidence of this at the moment, but I thought there were at least some thorns which would attempt to build anyway, even if you had set NO_BUILD. This would be the case if the thorn didn't know about the NO_BUILD option (external library handling is very nonuniform, with each library having to implement the same logic), but I thought it also happened for some thorns which did know about the option. I might be misremembering though.
On Mon, Aug 17, 2015 at 4:20 AM, Ian Hinder ian.hinder@aei.mpg.de wrote:
On 17 Aug 2015, at 08:21, Roland Haas rhaas@aei.mpg.de wrote:
Hello all,
This happens a lot. It would be good to be able to put something into the optionlist which told the MPI thorn that it should use an auto-detected library, rather than building the library.
Most thorns support a XXX_DIR=NO_BUILD option which then (depends on the thorn) may require you to actually specify the location of the libraries or may still allow searching for it. Basically all auto-detection (with the exception of MPI which also seems to fail here) should fail on modern Debian/Ubuntu systems that support "multi-arch" installations since the libraries are no longer in /usr/lib but in /usr/lib/x86-amd64 or so. Bruno was working on fixing this before the last release but the results were too fragile to be included in the current release branch.
I know about the NO_BUILD option, but was under the impression that it doesn't do or mean what it appears to mean. I can't find any evidence of this at the moment, but I thought there were at least some thorns which would attempt to build anyway, even if you had set NO_BUILD. This would be the case if the thorn didn't know about the NO_BUILD option (external library handling is very nonuniform, with each library having to implement the same logic), but I thought it also happened for some thorns which did know about the option. I might be misremembering though.
As Roland says, setting MPI_DIR = NO_BUILD should do the trick.
Apart from this -- yes, some thorns don't support NO_BUILD, e.g. thorns F5 or LORENE which always build from source.
-erik
On Fri, Aug 07, 2015 at 01:07:13PM -0400, Comer Duncan wrote:
attempting to build ET-Hilbert. The build goes ok until the end when I get some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem with MPI. I have openmpi installed as suggested at the top of the debian.cfg file.
Can you please send the complete build log? I am especially interested in the configure stage of the MPI thorn. It should have found the system MPI libraries. I did try the last release on a clean Jessie VM a while back, with only minimal packages installed, and that worked, if I recall correctly.
Also, please send what the following commands return:
which mpic++ mpic++ --showme
Frank
Hi Frank,
I am not sure I have mpic++ installed. I get nothing in response to which mpic++ :(((( .
I have pasted a build after adding OPEN_MPI_DIR=/usr and OPEN_MPI_LIB=-lmpi to the stock debian.cfg, but the result was about the same. Must be that I don't have the debian compilers I thought I had installed a couple of days ago. Here is the paste: http://pastebin.com/F806wUz5
Comer
On Fri, Aug 7, 2015 at 1:47 PM, Frank Loeffler knarf@cct.lsu.edu wrote:
On Fri, Aug 07, 2015 at 01:07:13PM -0400, Comer Duncan wrote:
attempting to build ET-Hilbert. The build goes ok until the end when I
get
some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem with MPI. I have openmpi installed as suggested at the top of the debian.cfg file.
Can you please send the complete build log? I am especially interested in the configure stage of the MPI thorn. It should have found the system MPI libraries. I did try the last release on a clean Jessie VM a while back, with only minimal packages installed, and that worked, if I recall correctly.
Also, please send what the following commands return:
which mpic++ mpic++ --showme
Frank
Here is what I have installed: perl gfortran g++ libopenmpi-dev openmpi-bin make libfftw3-dev libgsl0-dev libatlas-base-dev libjpeg-dev libssl-dev libhdf5-serial-dev hdf5-tools along with the rest of the stuff in debian.cfg. Isnt that basically what is needed?
Comer
On Fri, Aug 7, 2015 at 2:44 PM, Comer Duncan comer.duncan@gmail.com wrote:
Hi Frank,
I am not sure I have mpic++ installed. I get nothing in response to which mpic++ :(((( .
I have pasted a build after adding OPEN_MPI_DIR=/usr and OPEN_MPI_LIB=-lmpi to the stock debian.cfg, but the result was about the same. Must be that I don't have the debian compilers I thought I had installed a couple of days ago. Here is the paste: http://pastebin.com/F806wUz5
Comer
On Fri, Aug 7, 2015 at 1:47 PM, Frank Loeffler knarf@cct.lsu.edu wrote:
On Fri, Aug 07, 2015 at 01:07:13PM -0400, Comer Duncan wrote:
attempting to build ET-Hilbert. The build goes ok until the end when I
get
some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem
with
MPI. I have openmpi installed as suggested at the top of the debian.cfg file.
Can you please send the complete build log? I am especially interested in the configure stage of the MPI thorn. It should have found the system MPI libraries. I did try the last release on a clean Jessie VM a while back, with only minimal packages installed, and that worked, if I recall correctly.
Also, please send what the following commands return:
which mpic++ mpic++ --showme
Frank
Hi,
I have checked and installed (reinstalled) openmpi-dev with no changes to debian.cfg. Sorry for the noise. The thing builds and runs the static_tov test, so I think I've recovered from whatever was getting in the way. Thanks for help. By the way mpic++ is present and mpic++ --showme points to stuff that are in fact installed.
Comer
PS: I sort of like the debian jessie VM on my mac. It's pretty easy to go between debian and macosx and rsync is a pretty easy way to pass stuff between the two. The only problem i have is that I do not own Mathematica on the Paralles side :).
On Fri, Aug 7, 2015 at 2:55 PM, Comer Duncan comer.duncan@gmail.com wrote:
Here is what I have installed: perl gfortran g++ libopenmpi-dev openmpi-bin make libfftw3-dev libgsl0-dev libatlas-base-dev libjpeg-dev libssl-dev libhdf5-serial-dev hdf5-tools along with the rest of the stuff in debian.cfg. Isnt that basically what is needed?
Comer
On Fri, Aug 7, 2015 at 2:44 PM, Comer Duncan comer.duncan@gmail.com wrote:
Hi Frank,
I am not sure I have mpic++ installed. I get nothing in response to which mpic++ :(((( .
I have pasted a build after adding OPEN_MPI_DIR=/usr and OPEN_MPI_LIB=-lmpi to the stock debian.cfg, but the result was about the same. Must be that I don't have the debian compilers I thought I had installed a couple of days ago. Here is the paste: http://pastebin.com/F806wUz5
Comer
On Fri, Aug 7, 2015 at 1:47 PM, Frank Loeffler knarf@cct.lsu.edu wrote:
On Fri, Aug 07, 2015 at 01:07:13PM -0400, Comer Duncan wrote:
attempting to build ET-Hilbert. The build goes ok until the end when I
get
some complaints and then a make failure. I attach the output toward the end. I used the stock debian.cfg file. There seems to be a problem
with
MPI. I have openmpi installed as suggested at the top of the
debian.cfg
file.
Can you please send the complete build log? I am especially interested in the configure stage of the MPI thorn. It should have found the system MPI libraries. I did try the last release on a clean Jessie VM a while back, with only minimal packages installed, and that worked, if I recall correctly.
Also, please send what the following commands return:
which mpic++ mpic++ --showme
Frank
On 7 Aug 2015, at 19:07, Comer Duncan comer.duncan@gmail.com wrote:
I couple of days ago I bought Parallels for my mac and then installed debian jessie.
Hi,
Just to clarify: if you want to use Debian on a Mac, you can use VirtualBox, which is free (virtualbox.org). I didn't know that Parallels could run linux; mostly I think of it as something for running Windows (which you can also do with VirtualBox). I imagine Parallels is a bit more "polished". This is likely unrelated to your problem though, which should occur on either.
users@lists.einsteintoolkit.org
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Comer Duncan -
Erik Schnetter -
Frank Loeffler -
Ian Hinder -
Roland Haas