[Trilinos-Users] [EXTERNAL] help compiling shared libraries

Bradley, Andrew Michael ambradl at sandia.gov
Tue Jun 30 11:35:54 EDT 2015


Thanks Steven. That is quite helpful. We'll need to examine that issue.


In the meantime, Roger, turn this line off instead:

    -D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=OFF​


________________________________
From: Hamilton, Steven P. <hamiltonsp at ornl.gov>
Sent: Tuesday, June 30, 2015 9:31 AM
To: Phipps, Eric T; Roger Georges Ghanem; Bradley, Andrew Michael
Cc: trilinos-users at trilinos.org
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

Just to add an extra wrinkle to the issue, I was talking to a colleague this morning who said that he found the issue was tied to having explicit template instantiation enabled rather than due to shared vs. static libraries.  He was able to get around it by disabling ETI (at the cost of longer build times).  He also said that this was an issue on Mavericks, not just Yosemite.

--
Steven Hamilton
Radiation Transport Group
Reactor and Nuclear Systems Division
Oak Ridge National Laboratory
Phone: (865) 574-3646



From: <Phipps>, Eric T <etphipp at sandia.gov<mailto:etphipp at sandia.gov>>
Date: Tuesday, June 30, 2015 11:15 AM
To: Roger Georges Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>, "Bradley, Andrew Michael" <ambradl at sandia.gov<mailto:ambradl at sandia.gov>>
Cc: Steven Hamilton <hamiltonsp at ornl.gov<mailto:hamiltonsp at ornl.gov>>, "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

No.  You will still need to enable Thyra.

-Eric

From: Roger Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>
Date: Tuesday, June 30, 2015 at 9:14 AM
To: "Bradley, Andrew Michael" <ambradl at sandia.gov<mailto:ambradl at sandia.gov>>
Cc: Eric Phipps <etphipp at sandia.gov<mailto:etphipp at sandia.gov>>, "Hamilton, Steven P." <hamiltonsp at ornl.gov<mailto:hamiltonsp at ornl.gov>>, "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

To build Albany, do I need to also disable Thyra if I build static ?
Thanks


Sent from my iPhone

On Jun 30, 2015, at 8:09 AM, Bradley, Andrew Michael <ambradl at sandia.gov<mailto:ambradl at sandia.gov>> wrote:


Thanks all for the help on this.


Albany can build static. So if that ends up being the solution, at least for now, remove the

    -D BUILD_SHARED_LIBS:BOOL=ON \

line or set it to off in the Trilinos configuration. Then Albany will inherit the setting to do a static build.​


Andrew


________________________________
From: Trilinos-Users <trilinos-users-bounces at trilinos.org<mailto:trilinos-users-bounces at trilinos.org>> on behalf of Phipps, Eric T <etphipp at sandia.gov<mailto:etphipp at sandia.gov>>
Sent: Tuesday, June 30, 2015 8:51 AM
To: Phipps, Eric T; Roger Ghanem; Hamilton, Steven P.
Cc: trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

Can you also send your CMakeCache.txt file?

-Eric

From: <Phipps>, Eric Phipps <etphipp at sandia.gov<mailto:etphipp at sandia.gov>>
Date: Tuesday, June 30, 2015 at 8:48 AM
To: Roger Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>, "Hamilton, Steven P." <hamiltonsp at ornl.gov<mailto:hamiltonsp at ornl.gov>>
Cc: "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

Roger,

Can you send the output of 'make VERBOSE=1’ ? I would like to see how CMake is calling the linker.  It is possible we need to add/change a flag.

-Eric

From: Roger Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>
Date: Tuesday, June 30, 2015 at 7:37 AM
To: "Hamilton, Steven P." <hamiltonsp at ornl.gov<mailto:hamiltonsp at ornl.gov>>
Cc: "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries

Steven,

Will switching to static or disabling Thyra Impact my ability to build Albany ?
Thanks
Roger

Sent from my iPhone

On Jun 30, 2015, at 5:29 AM, Hamilton, Steven P. <hamiltonsp at ornl.gov<mailto:hamiltonsp at ornl.gov>> wrote:

We have a number of OS X users and have seen these Thyra virtual thunk errors repeatedly in Trilinos builds and TriBITS-based projects that use Trilinos.  I'm guessing you're using Yosemite?  We didn’t see this until people started upgrading from Mavericks to Yosemite.  If I recall correctly, the only workarounds we have found are to switch from shared to static libraries or to disable Thyra.  We noted this issue to a Thyra developer (not through this list), but last time we brought it up with him I don't think he had been able to reproduce the error.

- Steven

--
Steven Hamilton
Radiation Transport Group
Reactor and Nuclear Systems Division
Oak Ridge National Laboratory
Phone: (865) 574-3646



From: <Bradley>, Andrew Michael <ambradl at sandia.gov<mailto:ambradl at sandia.gov>>
Date: Monday, June 29, 2015 7:23 PM
To: Roger Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>, "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [Trilinos-Users] [EXTERNAL] help compiling shared libraries


Hi list,


Any OS X experts out there? These build failures have nothing to do with Albany; they have the form


Linking CXX shared library libthyracore.dylib
Undefined symbols for architecture x86_64:
  "virtual thunk to Thyra::VectorSpaceDefaultBase<std::complex<double> >::createMembers(int) const", referenced from:
      construction vtable for Thyra::VectorSpaceDefaultBase<std::complex<double> >-in-Thyra::DefaultMultiVectorProductVectorSpace<std::complex<double> > in Thyra_DefaultMultiVectorProductVectorSpace.cpp.o
      construction vtable for Thyra::VectorSpaceDefaultBase<std::complex<double> >-in-Thyra::DefaultProductVectorSpace<std::complex<double> > in Thyra_DefaultProductVectorSpace.cpp.o
      construction vtable for Thyra::VectorSpaceDefaultBase<std::complex<double> >-in-Thyra::DefaultClusteredSpmdProductVectorSpace<std::complex<double> > in Thyra_DefaultClusteredSpmdProductVectorSpace.cpp.o
      construction vtable for Thyra::VectorSpaceDefaultBase<std::complex<double> >-in-Thyra::DefaultSpmdVectorSpace<std::complex<double> > in Thyra_DefaultSpmdVectorSpace.cpp.o
      construction vtable for Thyra::ScalarProdVectorSpaceBase<std::complex<double> >-in-Thyra::DefaultSpmdVectorSpace<std::complex<double> > in Thyra_DefaultSpmdVectorSpace.cpp.o
      construction vtable for Thyra::SpmdVectorSpaceDefaultBase<std::complex<double> >-in-Thyra::DefaultSpmdVectorSpace<std::complex<double> > in Thyra_DefaultSpmdVectorSpace.cpp.o
      construction vtable for Thyra::VectorSpaceDefaultBase<std::complex<double> >-in-Thyra::SpmdVectorSpaceDefaultBase<std::complex<double> > in Thyra_SpmdVectorSpaceDefaultBase.cpp.o


I don't know what to make of these.


Thanks,

Andrew


________________________________
From: Roger Ghanem <ghanem at usc.edu<mailto:ghanem at usc.edu>>
Sent: Monday, June 29, 2015 5:12 PM
To: Bradley, Andrew Michael; trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: Re: [EXTERNAL] [Trilinos-Users] help compiling shared libraries

Hi Andrew,

I finally got around to another compile attempt.
I am attaching the script (which is very similar to the one from
https://github.com/gahansen/Albany/wiki/Albany:-Building-Trilinos

I am also attaching the errors I am still getting.

Any suggestion on what I may still be doing wrong ?

BTW:
On most previous attempts to compile Albany (with Trilinos 11.*)
under OSX I have had to modify slightly the source code (some variables
were apparently invoked without specifying a namespace).
gcc compilers under linux-*  did not complain.

Thanks
Roger



On 6/10/15 12:08 PM, Bradley, Andrew Michael wrote:

Hi Roger,


When was the previous time you updated Albany? Albany underwent three large transitions, one in about Aug or Sep 2014 (STKClassic -> STK), one on 6 Nov 2014 (Tpetra merge), and one on 24 Feb 2015 (Kokkos merge). In each transition, the build configuration changed.


Andrew


________________________________
From: Roger Ghanem <ghanem at usc.edu><mailto:ghanem at usc.edu>
Sent: Wednesday, June 10, 2015 1:06 PM
To: Bradley, Andrew Michael; trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: Re: [EXTERNAL] [Trilinos-Users] help compiling shared libraries

Anderw,
I updated Albany a couple of weeks ago. I have not been able to compile it since (against Trilinos12).
I have assumed these are troubles with Trilinos.
Roger


On 6/10/15 12:04 PM, Bradley, Andrew Michael wrote:

Hi Roger,


May I ask when you last updated Albany?


Otherwise, I agree: this might be an issue for the PyTrilinos experts.


Thanks,

Andrew


________________________________
From: Roger Ghanem <ghanem at usc.edu><mailto:ghanem at usc.edu>
Sent: Wednesday, June 10, 2015 1:01 PM
To: Bradley, Andrew Michael; trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: Re: [EXTERNAL] [Trilinos-Users] help compiling shared libraries

Andrew,

All was good with Trilinos 11.14.  Albany was compiling fine
with:
          -D Trilinos_ENABLE_STKUtil:BOOL=OFF \
          -D Trilinos_ENABLE_STKClassic:BOOL=ON \


The static libraries with Trilinos12. are building fine.
I have not tried compiling Albany yet.

I was compiling the shared library version of Trilinos
to add python functionality, which we found to be quite
useful also.  The make.log file  I sent you was for this
configuration.

Thanks
Roger


On 6/10/15 11:53 AM, Bradley, Andrew Michael wrote:

Hi Roger,


We may need multiple people to chime in. I'm seeing some errors having to do with multiple packages.


I see at the end of your email that you want to build Albany. I recommend following the guidance here:

    https://github.com/gahansen/Albany/wiki/Albany:-Building-Trilinos

In particular, you'll see that Albany uses STK rather than STKClassic. Building Trilinos with both STK and STKClassic is not possible, I'm fairly sure, so you'll want to use the STK flags provided in the link.

Cheers,

Andrew


________________________________
From: Trilinos-Users <trilinos-users-bounces at trilinos.org><mailto:trilinos-users-bounces at trilinos.org> on behalf of Roger G. Ghanem <ghanem at usc.edu><mailto:ghanem at usc.edu>
Sent: Wednesday, June 10, 2015 12:02 PM
To: trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>
Subject: [EXTERNAL] [Trilinos-Users] help compiling shared libraries

Dear Trilinos users,

I have attached the cmake configuration file and the make.log file from
a compilation attempt.

I am compiling on  OSX Yosemite.
I get the same error whether I am on mac pro or macbook air.
My environment is as follows:

gcc49 4.9.2_2
g++-mp-4.9
boost1.55
Python 2.7.10
cmake  3.2.2
Darwin Kernel Version 14.3.0
xnu-2782.20.48~5/RELEASE_X86_64 x86_64

ALSO:

1. I compiled the static version successfully (clearly it lacks Python functionality).

2. In the shared version, I have to manually edit the two link files:

packages/stk/stk_classic/stk_util/stk_util/environment/CMakeFiles/stkclassic_util_env.dir/link.txt

adding:  ../parallel/libstkclassic_util_parallel.dylib

and

packages/stk/stk_classic//stk_util/stk_util/unit_test_support/CMakeFiles/stkclassic_util_unit_test_support.dir/link.txt

adding: ../util/libstkclassic_util_util.dylib


ALSO:
when including MeshingGenie, it compiled properly.  But when I tried to compile
Albany, I was informed that      MeshingGenieConfig.cmake      could not be found.
Indeed I could not find that file in the build or install directories.


Thank you for your help.
Roger

--
---------------------------------
Roger Ghanem
210 KAP Hall
University of Southern California
Los Angeles, CA 90089
Tel: 213 740 9528



--
Roger Ghanem
210 KAP Hall
University of Southern California
Los Angeles, CA 90089


--
Roger Ghanem
210 KAP Hall
University of Southern California
Los Angeles, CA 90089


--
---------------------------------
Roger Ghanem
210 KAP Hall
University of Southern California
Los Angeles, CA 90089
Tel: 213 740 9528

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