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

Roger Ghanem ghanem at usc.edu
Tue Jun 30 18:10:15 EDT 2015 

Andrew,

git log
shows:
commit 8cc9d0c499891e4c97bd6530677f85728e1fe3fb

Roger


On 6/30/15 2:51 PM, Bradley, Andrew Michael wrote:
>
> Hi Roger,
>
>
> What ALbany SHA1 (the hash code at the top of "git log") are you building?
>
>
> Thanks,
> Andrew
>
>
> ------------------------------------------------------------------------
> *From:* Roger Ghanem <ghanem at usc.edu>
> *Sent:* Tuesday, June 30, 2015 3:48 PM
> *To:* Phipps, Eric T; Bradley, Andrew Michael
> *Cc:* Hamilton, Steven P.; trilinos-users at trilinos.org
> *Subject:* Re: [Trilinos-Users] [EXTERNAL] help compiling shared 
> libraries
> Eric,
>
> With SHARE=OFF
>       and Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=OFF​
> I was able to compile Trilinos.  But please read on for possible
> errors in the build/install.
>
> Compiling Albany, I got into trouble very early on.
> I am attaching the configure, CMakeCache.txt
> and two make.log files:
>
> One of them obtained from
> make VERBOSE=1
> and the other using
> make -j 10 VERBOSE=1    looks ahead and catches a few more errors.
>
> Phalanx_ConfigDefs.hpp   was not found because it not
> in ALBANY_TRILINOS_DIR/include
> when I copied it from the source tree into the Trilinos 
> distribution/include,
> I got another error about:
> Phalanx_Allocator_Contiguous.hpp  not being found.  I could not locate 
> that
> file in the source tree or build tree.  (I could find this file in 
> Trilinos11.10 at:
> source/packages/phalanx/src/Phalanx_Allocator_Contiguous.hpp
>
> stk_mesh/fem/CoordinateSystems.hpp    was not found
> because  it is in  stk_mesh/base/CoordinateSystems.hpp
> stk_mesh/fem  was not created in ALBANY_TRILINOS_DIR
> (it was created under Trilinos11.10 - but that was probably STK_CLASSIC)
>
> Thanks again
> Roger
>
>
> On 6/30/15 8:15 AM, Phipps, Eric T wrote:
>> 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>
>>>>> *Sent:* Wednesday, June 10, 2015 1:06 PM
>>>>> *To:* Bradley, Andrew Michael; 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>
>>>>>> *Sent:* Wednesday, June 10, 2015 1:01 PM
>>>>>> *To:* Bradley, Andrew Michael; 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> on 
>>>>>>> behalf of Roger G. Ghanem <ghanem at usc.edu>
>>>>>>> *Sent:* Wednesday, June 10, 2015 12:02 PM
>>>>>>> *To:* 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
>
> -- 
> 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

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