Nektar++-4.3.3 compilation errors
Dear All, I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error: In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0, from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36: /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type const string uds) ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type string m_udsfile; ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)': /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile' m_verbose(ver), m_udsfile(uds) ^ library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1 CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 This error showed up when compiling the 4.3.2 version of the code too. What could I be doing wrong, and how can I resolve it? Looking forward to hearing from you soon. Thank you, Manish Sharma
Dear Manish, It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release. One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help. Cheers, Douglas ________________________________ From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu> Sent: 23 August 2016 23:09:06 To: nektar-users Subject: [Nektar-users] Nektar++-4.3.3 compilation errors Dear All, I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error: In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0, from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36: /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type const string uds) ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type string m_udsfile; ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)': /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile' m_verbose(ver), m_udsfile(uds) ^ library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1 CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 This error showed up when compiling the 4.3.2 version of the code too. What could I be doing wrong, and how can I resolve it? Looking forward to hearing from you soon. Thank you, Manish Sharma
Thank you very much, Douglas, for providing this solution. I will use your suggestions and compile the code. Manish From: Serson, Douglas [mailto:d.serson14@imperial.ac.uk] Sent: Tuesday, August 23, 2016 6:35 PM To: Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> Subject: Re: Nektar++-4.3.3 compilation errors Dear Manish, It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release. One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help. Cheers, Douglas ________________________________ From: nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu<mailto:sharmamh@mail.uc.edu>> Sent: 23 August 2016 23:09:06 To: nektar-users Subject: [Nektar-users] Nektar++-4.3.3 compilation errors Dear All, I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error: In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0, from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36: /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type const string uds) ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type string m_udsfile; ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)': /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile' m_verbose(ver), m_udsfile(uds) ^ library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1 CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 This error showed up when compiling the 4.3.2 version of the code too. What could I be doing wrong, and how can I resolve it? Looking forward to hearing from you soon. Thank you, Manish Sharma
Dear Douglas, I took your advice and downloaded the master branch from the repository. The code had almost compiled, except at the end it gave the following error: make[2]: *** No rule to make target '/usr/lib64/libpython2.7.so', needed by 'utilities/Extras/VtkToPng'. Stop. CMakeFiles/Makefile2:5919: recipe for target 'utilities/Extras/CMakeFiles/VtkToPng.dir/all' failed make[1]: *** [utilities/Extras/CMakeFiles/VtkToPng.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2 What could the reason for this error might be, and how can I resolve it? I greatly appreciate your help for this. Thank you. Manish ________________________________ From: Sharma, Manish (sharmamh) Sent: Tuesday, August 23, 2016 6:44:07 PM To: Serson, Douglas; nektar-users Subject: RE: Nektar++-4.3.3 compilation errors Thank you very much, Douglas, for providing this solution. I will use your suggestions and compile the code. Manish From: Serson, Douglas [mailto:d.serson14@imperial.ac.uk] Sent: Tuesday, August 23, 2016 6:35 PM To: Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> Subject: Re: Nektar++-4.3.3 compilation errors Dear Manish, It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release. One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help. Cheers, Douglas ________________________________ From: nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu<mailto:sharmamh@mail.uc.edu>> Sent: 23 August 2016 23:09:06 To: nektar-users Subject: [Nektar-users] Nektar++-4.3.3 compilation errors Dear All, I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error: In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0, from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36: /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type const string uds) ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type string m_udsfile; ^ /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)': /home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile' m_verbose(ver), m_udsfile(uds) ^ library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1 CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2 Makefile:146: recipe for target 'all' failed make: *** [all] Error 2 This error showed up when compiling the 4.3.2 version of the code too. What could I be doing wrong, and how can I resolve it? Looking forward to hearing from you soon. Thank you, Manish Sharma
Hi Manish, This will depend on which exact operating system, but you probably want to install the libpython2.7-dev or python-devel package. This should provide the libpython2.7.so file which is missing on your system. Cheers, Chris On 24/08/16 19:59, Sharma, Manish (sharmamh) wrote:
Dear Douglas,
I took your advice and downloaded the master branch from the repository. The code had almost compiled, except at the end it gave the following error:
make[2]: *** No rule to make target '/usr/lib64/libpython2.7.so', needed by 'utilities/Extras/VtkToPng'. Stop. CMakeFiles/Makefile2:5919: recipe for target 'utilities/Extras/CMakeFiles/VtkToPng.dir/all' failed make[1]: *** [utilities/Extras/CMakeFiles/VtkToPng.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2
What could the reason for this error might be, and how can I resolve it?
I greatly appreciate your help for this. Thank you.
Manish
------------------------------------------------------------------------
*From:*Sharma, Manish (sharmamh) *Sent:* Tuesday, August 23, 2016 6:44:07 PM *To:* Serson, Douglas; nektar-users *Subject:* RE: Nektar++-4.3.3 compilation errors
Thank you very much, Douglas, for providing this solution.
I will use your suggestions and compile the code.
Manish
*From:* Serson, Douglas [mailto:d.serson14@imperial.ac.uk] *Sent:* Tuesday, August 23, 2016 6:35 PM *To:* Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> *Subject:* Re: Nektar++-4.3.3 compilation errors
Dear Manish,
It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release.
One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help.
Cheers,
Douglas
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu <mailto:sharmamh@mail.uc.edu>> *Sent:* 23 August 2016 23:09:06 *To:* nektar-users *Subject:* [Nektar-users] Nektar++-4.3.3 compilation errors
Dear All,
I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error:
In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0,
from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: ‘string’ does not name a type
const string uds)
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: ‘string’ does not name a type
string m_udsfile;
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor ‘Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)’:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class ‘Nektar::NekMeshUtils::Octree’ does not have any field named ‘m_udsfile’
m_verbose(ver), m_udsfile(uds)
^
library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed
make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1
CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed
make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2
This error showed up when compiling the 4.3.2 version of the code too.
What could I be doing wrong, and how can I resolve it?
Looking forward to hearing from you soon.
Thank you,
Manish Sharma
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- 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 Chris, Thanks for your help. I was able to successfully recompile the code after installing the python-devel package. However, when I ran the ctest, all except two tests passed, and this is the output I received: 99% tests passed, 2 tests failed out of 413 Total Test time (real) = 507.93 sec The following tests FAILED: 412 - NekMesh_MeshGen/cylinder (Failed) 413 - NekMesh_MeshGen/sphere (Failed) Errors while running CTest What could be the reason for this? Thank you, Manish ________________________________ From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Chris Cantwell <c.cantwell@imperial.ac.uk> Sent: Wednesday, August 24, 2016 4:27:04 PM To: nektar-users@imperial.ac.uk Subject: Re: [Nektar-users] Nektar++-4.3.3 compilation errors Hi Manish, This will depend on which exact operating system, but you probably want to install the libpython2.7-dev or python-devel package. This should provide the libpython2.7.so file which is missing on your system. Cheers, Chris On 24/08/16 19:59, Sharma, Manish (sharmamh) wrote:
Dear Douglas,
I took your advice and downloaded the master branch from the repository. The code had almost compiled, except at the end it gave the following error:
make[2]: *** No rule to make target '/usr/lib64/libpython2.7.so', needed by 'utilities/Extras/VtkToPng'. Stop. CMakeFiles/Makefile2:5919: recipe for target 'utilities/Extras/CMakeFiles/VtkToPng.dir/all' failed make[1]: *** [utilities/Extras/CMakeFiles/VtkToPng.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2
What could the reason for this error might be, and how can I resolve it?
I greatly appreciate your help for this. Thank you.
Manish
------------------------------------------------------------------------
*From:*Sharma, Manish (sharmamh) *Sent:* Tuesday, August 23, 2016 6:44:07 PM *To:* Serson, Douglas; nektar-users *Subject:* RE: Nektar++-4.3.3 compilation errors
Thank you very much, Douglas, for providing this solution.
I will use your suggestions and compile the code.
Manish
*From:* Serson, Douglas [mailto:d.serson14@imperial.ac.uk] *Sent:* Tuesday, August 23, 2016 6:35 PM *To:* Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> *Subject:* Re: Nektar++-4.3.3 compilation errors
Dear Manish,
It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release.
One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help.
Cheers,
Douglas
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu <mailto:sharmamh@mail.uc.edu>> *Sent:* 23 August 2016 23:09:06 *To:* nektar-users *Subject:* [Nektar-users] Nektar++-4.3.3 compilation errors
Dear All,
I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error:
In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0,
from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type
const string uds)
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type
string m_udsfile;
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)':
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile'
m_verbose(ver), m_udsfile(uds)
^
library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed
make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1
CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed
make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2
This error showed up when compiling the 4.3.2 version of the code too.
What could I be doing wrong, and how can I resolve it?
Looking forward to hearing from you soon.
Thank you,
Manish Sharma
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell<http://www.imperial.ac.uk/people/c.cantwell> _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Manish, Could you run ctest with an additional option as follows: ctest --output-on-failure -R NekMesh and send me the output? There should also be files generated in sub-directories within build/utilities/NekMesh. If you can send me those, they may also prove useful. Cheers, Chris On 26/08/16 00:29, Sharma, Manish (sharmamh) wrote:
Hi Chris,
Thanks for your help.
I was able to successfully recompile the code after installing the python-devel package. However, when I ran the ctest, all except two tests passed, and this is the output I received:
99% tests passed, 2 tests failed out of 413
Total Test time (real) = 507.93 sec
The following tests FAILED: 412 - NekMesh_MeshGen/cylinder (Failed) 413 - NekMesh_MeshGen/sphere (Failed) Errors while running CTest
What could be the reason for this?
Thank you,
Manish
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Chris Cantwell <c.cantwell@imperial.ac.uk> *Sent:* Wednesday, August 24, 2016 4:27:04 PM *To:* nektar-users@imperial.ac.uk *Subject:* Re: [Nektar-users] Nektar++-4.3.3 compilation errors
Hi Manish,
This will depend on which exact operating system, but you probably want to install the libpython2.7-dev or python-devel package. This should provide the libpython2.7.so file which is missing on your system.
Cheers, Chris
On 24/08/16 19:59, Sharma, Manish (sharmamh) wrote:
Dear Douglas,
I took your advice and downloaded the master branch from the repository. The code had almost compiled, except at the end it gave the following error:
make[2]: *** No rule to make target '/usr/lib64/libpython2.7.so', needed by 'utilities/Extras/VtkToPng'. Stop. CMakeFiles/Makefile2:5919: recipe for target 'utilities/Extras/CMakeFiles/VtkToPng.dir/all' failed make[1]: *** [utilities/Extras/CMakeFiles/VtkToPng.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2
What could the reason for this error might be, and how can I resolve it?
I greatly appreciate your help for this. Thank you.
Manish
------------------------------------------------------------------------
*From:*Sharma, Manish (sharmamh) *Sent:* Tuesday, August 23, 2016 6:44:07 PM *To:* Serson, Douglas; nektar-users *Subject:* RE: Nektar++-4.3.3 compilation errors
Thank you very much, Douglas, for providing this solution.
I will use your suggestions and compile the code.
Manish
*From:* Serson, Douglas [mailto:d.serson14@imperial.ac.uk] *Sent:* Tuesday, August 23, 2016 6:35 PM *To:* Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> *Subject:* Re: Nektar++-4.3.3 compilation errors
Dear Manish,
It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release.
One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help.
Cheers,
Douglas
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu <mailto:sharmamh@mail.uc.edu>> *Sent:* 23 August 2016 23:09:06 *To:* nektar-users *Subject:* [Nektar-users] Nektar++-4.3.3 compilation errors
Dear All,
I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error:
In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0,
from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: ‘string’ does not name a type
const string uds)
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: ‘string’ does not name a type
string m_udsfile;
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor ‘Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)’:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class ‘Nektar::NekMeshUtils::Octree’ does not have any field named ‘m_udsfile’
m_verbose(ver), m_udsfile(uds)
^
library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed
make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1
CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed
make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2
This error showed up when compiling the 4.3.2 version of the code too.
What could I be doing wrong, and how can I resolve it?
Looking forward to hearing from you soon.
Thank you,
Manish Sharma
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-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell <http://www.imperial.ac.uk/people/c.cantwell>
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-- 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 Chris, Here is the output and attached are the files from tmp_cylinder and tmp_sphere subdirectories within build/utilities/NekMesh: Start 412: NekMesh_MeshGen/cylinder 21/22 Test #412: NekMesh_MeshGen/cylinder ........................***Failed 26.96 sec sh: line 1: 55068 Aborted /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/NekMesh -m jac:list cylinder.mcf cylinder.xml:xml:test > output.out 2> output.err Error occurred running test: Command: /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/NekMesh -m jac:list cylinder.mcf cylinder.xml:xml:test 1>output.out 2>output.err Files left in /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/tmp_cylinder Start 413: NekMesh_MeshGen/sphere 22/22 Test #413: NekMesh_MeshGen/sphere ..........................***Failed 13.46 sec sh: line 1: 55123 Aborted /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/NekMesh -m jac:list sphere.mcf sphere.xml:xml:test > output.out 2> output.err Error occurred running test: Command: /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/NekMesh -m jac:list sphere.mcf sphere.xml:xml:test 1>output.out 2>output.err Files left in /media/sda7/sharmamh/nektar-master/build/utilities/NekMesh/tmp_sphere 91% tests passed, 2 tests failed out of 22 Total Test time (real) = 64.44 sec The following tests FAILED: 412 - NekMesh_MeshGen/cylinder (Failed) 413 - NekMesh_MeshGen/sphere (Failed) Errors while running CTest Are there any other specific files that you need from the NekMesh directory, as there are many in it? Let me know if you do. Thank you, Manish ________________________________ From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Chris Cantwell <c.cantwell@imperial.ac.uk> Sent: Friday, August 26, 2016 3:20:47 AM To: nektar-users@imperial.ac.uk Subject: Re: [Nektar-users] Nektar++-4.3.3 compilation errors Hi Manish, Could you run ctest with an additional option as follows: ctest --output-on-failure -R NekMesh and send me the output? There should also be files generated in sub-directories within build/utilities/NekMesh. If you can send me those, they may also prove useful. Cheers, Chris On 26/08/16 00:29, Sharma, Manish (sharmamh) wrote:
Hi Chris,
Thanks for your help.
I was able to successfully recompile the code after installing the python-devel package. However, when I ran the ctest, all except two tests passed, and this is the output I received:
99% tests passed, 2 tests failed out of 413
Total Test time (real) = 507.93 sec
The following tests FAILED: 412 - NekMesh_MeshGen/cylinder (Failed) 413 - NekMesh_MeshGen/sphere (Failed) Errors while running CTest
What could be the reason for this?
Thank you,
Manish
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Chris Cantwell <c.cantwell@imperial.ac.uk> *Sent:* Wednesday, August 24, 2016 4:27:04 PM *To:* nektar-users@imperial.ac.uk *Subject:* Re: [Nektar-users] Nektar++-4.3.3 compilation errors
Hi Manish,
This will depend on which exact operating system, but you probably want to install the libpython2.7-dev or python-devel package. This should provide the libpython2.7.so file which is missing on your system.
Cheers, Chris
On 24/08/16 19:59, Sharma, Manish (sharmamh) wrote:
Dear Douglas,
I took your advice and downloaded the master branch from the repository. The code had almost compiled, except at the end it gave the following error:
make[2]: *** No rule to make target '/usr/lib64/libpython2.7.so', needed by 'utilities/Extras/VtkToPng'. Stop. CMakeFiles/Makefile2:5919: recipe for target 'utilities/Extras/CMakeFiles/VtkToPng.dir/all' failed make[1]: *** [utilities/Extras/CMakeFiles/VtkToPng.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2
What could the reason for this error might be, and how can I resolve it?
I greatly appreciate your help for this. Thank you.
Manish
------------------------------------------------------------------------
*From:*Sharma, Manish (sharmamh) *Sent:* Tuesday, August 23, 2016 6:44:07 PM *To:* Serson, Douglas; nektar-users *Subject:* RE: Nektar++-4.3.3 compilation errors
Thank you very much, Douglas, for providing this solution.
I will use your suggestions and compile the code.
Manish
*From:* Serson, Douglas [mailto:d.serson14@imperial.ac.uk] *Sent:* Tuesday, August 23, 2016 6:35 PM *To:* Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu>; nektar-users <nektar-users@imperial.ac.uk> *Subject:* Re: Nektar++-4.3.3 compilation errors
Dear Manish,
It looks like this is caused by a bug which is already fixed in our master branch, but unfortunately the fix is not in the latest release.
One solution is to get the master branch from the repository. Alternatively, I think this is only a problem when compiling with the NEKTAR_USE_MESHGEN option. If you don't need this functionality, switching it off in cmake should help.
Cheers,
Douglas
------------------------------------------------------------------------
*From:*nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk <mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Sharma, Manish (sharmamh) <sharmamh@mail.uc.edu <mailto:sharmamh@mail.uc.edu>> *Sent:* 23 August 2016 23:09:06 *To:* nektar-users *Subject:* [Nektar-users] Nektar++-4.3.3 compilation errors
Dear All,
I am trying to compile the latest version of the code, nektar++-4.3.3, and I am getting the following error:
In file included from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.h:44:0,
from /home/manish/nektar++-4.3.3/library/NekMeshUtils/SurfaceMeshing/CurveMesh.cpp:36:
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:76:18: error: 'string' does not name a type
const string uds)
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:183:5: error: 'string' does not name a type
string m_udsfile;
^
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h: In constructor 'Nektar::NekMeshUtils::Octree::Octree(Nektar::NekMeshUtils::CADSystemSharedPtr, bool, Nektar::NekDouble, Nektar::NekDouble, Nektar::NekDouble, int)':
/home/manish/nektar++-4.3.3/library/NekMeshUtils/Octree/Octree.h:78:27: error: class 'Nektar::NekMeshUtils::Octree' does not have any field named 'm_udsfile'
m_verbose(ver), m_udsfile(uds)
^
library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/build.make:307: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o' failed
make[2]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/SurfaceMeshing/CurveMesh.cpp.o] Error 1
CMakeFiles/Makefile2:904: recipe for target 'library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all' failed
make[1]: *** [library/NekMeshUtils/CMakeFiles/NekMeshUtils.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2
This error showed up when compiling the 4.3.2 version of the code too.
What could I be doing wrong, and how can I resolve it?
Looking forward to hearing from you soon.
Thank you,
Manish Sharma
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell<http://www.imperial.ac.uk/people/c.cantwell> <http://www.imperial.ac.uk/people/c.cantwell>
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell<http://www.imperial.ac.uk/people/c.cantwell> _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
participants (3)
-
Chris Cantwell
-
Serson, Douglas
-
Sharma, Manish (sharmamh)