Re: [Nektar-users] FW: Problem while installing nektar++ with lapack
Hi Jeremy, I'm actually trying to build nektar++ on a BGQ cluster similar to Mira. I'm trying to build nektar++-4.4.1 and the system lapacek version is 3.4.2 Sincerely, On Fri, Oct 12, 2018 at 4:24 AM Amitvikram Dutta < amitvikram.dutta@uwaterloo.ca> wrote:
------------------------------ *From:* nektar-users-bounces@imperial.ac.ukOn Behalf OfJeremy Cohen *Sent:* October 12, 2018 4:24:33 AM (UTC-05:00) Eastern Time (US & Canada) *To:* Amitvikram Dutta *Cc:* nektar-users *Subject:* Re: [Nektar-users] Problem while installing nektar++ with lapack
Hi Amitvikram,
Can you provide some further details of the problem you're encountering.
Specifically, can you confirm what platform (including version) you're building on, and if Linux, which I assume is the platform you're using, which distribution.
Can you also confirm what version of Nektar++ you're trying to build, and the version of the system Lapack distribution that you're using.
Thanks,
Jeremy
On 12 Oct 2018, at 01:05, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi all,
I keep having the same problem while trying to install nektar++ with regards to the Lapack libraries.
When I try to use the system Lapack installation I get the following message
*/scinet/bgq/Libraries/lapack/lib/liblapack.so: undefined reference to `_xlfEndIO@XLF_1.0'*
while when I try to install using the ThirdParty Lapack supplied with the nektar++ source directory I get the following error
*../../library/LibUtilities/libLibUtilities.so.4.4.1: undefined reference to `dtpmv_'*
I have a feeling these errors have been encountered by the community at large before. Could someone point out where I'm going wrong?
Sincerely, --
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
--
*Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo
Hi Amitvikram, Could you send us your CMakeCache.txt file from your build directory and the output from running: make VERBOSE=1 for both cases. In the case of using ThirdParty LAPACK, it seems to not be linking to it. Probably you should be using vendor-supplied libraries if possible though so better if ee can get those working. Thanks, Chris On 12 October 2018 14:08:55 BST, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi Jeremy,
I'm actually trying to build nektar++ on a BGQ cluster similar to Mira.
I'm trying to build nektar++-4.4.1 and the system lapacek version is 3.4.2
Sincerely, On Fri, Oct 12, 2018 at 4:24 AM Amitvikram Dutta < amitvikram.dutta@uwaterloo.ca> wrote:
------------------------------ *From:* nektar-users-bounces@imperial.ac.ukOn Behalf OfJeremy Cohen *Sent:* October 12, 2018 4:24:33 AM (UTC-05:00) Eastern Time (US &
Canada)
*To:* Amitvikram Dutta *Cc:* nektar-users *Subject:* Re: [Nektar-users] Problem while installing nektar++ with lapack
Hi Amitvikram,
Can you provide some further details of the problem you're encountering.
Specifically, can you confirm what platform (including version) you're building on, and if Linux, which I assume is the platform you're using, which distribution.
Can you also confirm what version of Nektar++ you're trying to build, and the version of the system Lapack distribution that you're using.
Thanks,
Jeremy
On 12 Oct 2018, at 01:05, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi all,
I keep having the same problem while trying to install nektar++ with regards to the Lapack libraries.
When I try to use the system Lapack installation I get the following message
*/scinet/bgq/Libraries/lapack/lib/liblapack.so: undefined reference to `_xlfEndIO@XLF_1.0'*
while when I try to install using the ThirdParty Lapack supplied with the nektar++ source directory I get the following error
*../../library/LibUtilities/libLibUtilities.so.4.4.1: undefined reference to `dtpmv_'*
I have a feeling these errors have been encountered by the community at large before. Could someone point out where I'm going wrong?
Sincerely, --
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
--
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
Hi Amitvikram, As Chris suggests, it's probably better to use vendor supplied libraries if you can get those working. In addition to the further information Chris has asked to take a look at, one thing you could check is to whether there are any files in your nektar++/build/ThirdParty/lapack-3.7.0 directory (if that directory exists at all). I've been trying to see if I can recreate the problem and I was able to see something similar when setting THIRDPARTY_BUILD_BLAS_LAPACK=ON and NEKTAR_USE_SYSTEM_BLAS_LAPACK=OFF. In this case, I can configure successfully and start the build but it fails with a large number of undefined references that are similar to, and include, the dtpmv_ symbol that you mentioned. When I look in nektar++/build/ThirdParty/lapack-3.7.0, the directory is empty so it looks like the build system has configured on the basis of building its own blas/lapack but the build hasn't been carried out and therefore LibUtilities can't be linked against it. As a test, you could try running the build with both THIRDPARTY_BUILD_BLAS_LAPACK=ON and NEKTAR_USE_SYSTEM_BLAS_LAPACK=ON, if this isn't the setting you've been using already. When I tried this, the build of blas/lapack is carried out successfully and the linking is fine with the full build of Nektar++ completing successfully. I removed the system blas/lapack on my test system to be sure it was linking against the correct instance. Cheers, Jeremy On 12 Oct 2018, at 17:50, Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
Hi Amitvikram,
Could you send us your CMakeCache.txt file from your build directory and the output from running: make VERBOSE=1 for both cases.
In the case of using ThirdParty LAPACK, it seems to not be linking to it. Probably you should be using vendor-supplied libraries if possible though so better if ee can get those working.
Thanks, Chris
On 12 October 2018 14:08:55 BST, Amitvikram Dutta <amitvdutta23@gmail.com> wrote: Hi Jeremy,
I'm actually trying to build nektar++ on a BGQ cluster similar to Mira.
I'm trying to build nektar++-4.4.1 and the system lapacek version is 3.4.2
Sincerely, On Fri, Oct 12, 2018 at 4:24 AM Amitvikram Dutta <amitvikram.dutta@uwaterloo.ca> wrote:
From: nektar-users-bounces@imperial.ac.ukOn Behalf OfJeremy Cohen Sent: October 12, 2018 4:24:33 AM (UTC-05:00) Eastern Time (US & Canada) To: Amitvikram Dutta Cc: nektar-users Subject: Re: [Nektar-users] Problem while installing nektar++ with lapack
Hi Amitvikram,
Can you provide some further details of the problem you're encountering.
Specifically, can you confirm what platform (including version) you're building on, and if Linux, which I assume is the platform you're using, which distribution.
Can you also confirm what version of Nektar++ you're trying to build, and the version of the system Lapack distribution that you're using.
Thanks,
Jeremy
On 12 Oct 2018, at 01:05, Amitvikram Dutta <amitvdutta23@gmail.com> wrote:
Hi all,
I keep having the same problem while trying to install nektar++ with regards to the Lapack libraries.
When I try to use the system Lapack installation I get the following message
/scinet/bgq/Libraries/lapack/lib/liblapack.so: undefined reference to `_xlfEndIO@XLF_1.0'
while when I try to install using the ThirdParty Lapack supplied with the nektar++ source directory I get the following error
../../library/LibUtilities/libLibUtilities.so.4.4.1: undefined reference to `dtpmv_'
I have a feeling these errors have been encountered by the community at large before. Could someone point out where I'm going wrong?
Sincerely, -- Amitvikram Dutta
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Amitvikram Dutta
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
participants (3)
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Amitvikram Dutta
-
Chris Cantwell
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Jeremy Cohen