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

Roger Ghanem ghanem at usc.edu
Tue Jun 30 18:23:32 EDT 2015 

Andrew,
I did a clone a couple of weeks ago.
I just did another clone
with the same log:
commit 8cc9d0c499891e4c97bd6530677f85728e1fe3fb

I am cloning from:  software.sandia.gov:/space/git/Albany

Roger


On 6/30/15 3:17 PM, Bradley, Andrew Michael wrote:
>
> Hi Roger,
>
>
> 18 Aug 2014, right?
>
>
> I don't think git pull will even work, as we had a branch switch in 
> Nov in which a big merge failed for messy historical reasons. So do a 
> fresh "git clone".
>
>
> Andrew
>
>
> ------------------------------------------------------------------------
> *From:* Roger Ghanem <ghanem at usc.edu>
> *Sent:* Tuesday, June 30, 2015 4:10 PM
> *To:* Bradley, Andrew Michael; Phipps, Eric T
> *Cc:* Hamilton, Steven P.; trilinos-users at trilinos.org
> *Subject:* Re: [Trilinos-Users] [EXTERNAL] help compiling shared 
> libraries
> 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

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

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