Fluidity

Error during "make" of fluidity after configure

Asked by S Ueda

Hi,

I am trying to install and run Fluidity on UBUNTU 14.04 PC and I am facing the issue during "make" of Fluidity. Owing to the helpful advice regarding the PETCs library, I could configure fluidity after "sudo apt-get install petsc-dev". Then, I tried "make", but it gave the following error.

Error was:
./lib/libspatialindex.a(Tools.o): In function `Tools::TemporaryFile::TemporaryFile()':
Tools.cc:(.text+0x304c): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
./lib/libadaptivity.a(ParMetis.o): In function `csr::Graph::RepartRemap(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)':
ParMetis.cpp:(.text+0x37e): undefined reference to `ParMETIS_V3_AdaptiveRepart'
./lib/libadaptivity.a(ParMetis.o): In function `csr::Graph::Repart(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, int)':
ParMetis.cpp:(.text+0x8a4): undefined reference to `ParMETIS_V3_PartKway'
collect2: error: ld returned 1 exit status
----
make: *** [bin/fluidity] Error 1

 Is this a general error related to libraries or do I have to modify the source code of fluidity?
I would like to solve this issue with your kind help.

Thank you
sueda

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Tim Greaves
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Best Tim Greaves (tim-greaves) said : 		#1

Hi Sueda,

It sounds like you have conflicting versions of ParMetis installed there. My advice would be to make sure you have the fluidity-dev package installed from the fluidity-core ppa ( https://launchpad.net/~fluidity-core/+archive/ubuntu/ppa ) and make sure versions of ParMetis other than that installed with the PETSc 3.6.3 package are removed from default system paths. My guess would be that you have a system ParMetis v.3 package which libadaptivity is building against, whereas at linking time v.4 is present through PETSc.

Also - please could I refer you to: https://github.com/FluidityProject/fluidity/issues

We've not used Launchpad as our primary development site for some time now, having migrated to GitHub.

Thanks and best wishes,

Tim

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S Ueda (sueda) said : 		#2

Hi Tim Greaves,

Thank you for your quick response and good advice.

>> It sounds like you have conflicting versions of ParMetis installed there. My advice would be to make sure you have the
>> fluidity-dev package installed from the fluidity-core ppa ( https://launchpad.net/~fluidity-core/+archive/ubuntu/ppa ) and make >> sure versions of ParMetis other than that installed with the PETSc 3.6.3 package are removed from default system paths. My
>> guess would be that you have a system ParMetis v.3 package which libadaptivity is building against, whereas at linking time v.4 is
>> present through PETSc.

I made sure that I have the fluidity-dev package with the command "sudo apt-get install fluidity-dev". In addition, I also installed ParMetis v.4 (ParMetis -4.0.3). Then, I configured again and it was finished this time. I could run fluidity and run "top_hat" and "driven_cavity" in examples.

However, I faced an error in "water_collapse". This seems to be related with MPI_ABORT. I will try to solve it with reading the contents in the following GitHub site which you kindly showed to me.

>> Also - please could I refer you to: https://github.com/FluidityProject/fluidity/issues
>>
>> We've not used Launchpad as our primary development site for some time now, having migrated to GitHub.

Thank you for introducing above site to me.

Finally, thank you again for your kindness and good advice.

Yours sincerely,
Sueda

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S Ueda (sueda) said : 		#3

Thanks Tim Greaves, that solved my question.