Error once I have compiled ASPECT

ASPECT
1

Hi everyone, my name is Pedro. I think I have installed and compiled ASPECT succesfully. When I run make, it reaches the 100 . This message is displayed: [100] Linking CXX executable aspect
[100%] Built target aspect
However, when I write ‘make test’, the following error is displayed:

bash-3.2$ make test

Consolidate compiler generated dependencies of target aspect

[ 98%] Built target aspect

[100%] Running unit_tests …

/bin/sh: line 1: 3869 Illegal instruction: 4 /Users/pedro_gea/aspect/release/aspect --test

make[3]: *** [CMakeFiles/run_unit_tests] Error 132

make[2]: *** [CMakeFiles/run_unit_tests.dir/all] Error 2

make[1]: *** [CMakeFiles/test.dir/rule] Error 2

make: *** [test] Error 2

bash-3.2$

Also, when I run a .prm file using mpi, I get the following error:

Primary job terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

mpirun noticed that process rank 1 with PID 0 on node cvi067009 exited on signal 4 (Illegal instruction: 4).

Any ideas as to the cause of the problem?
Pedro

2

Hi Pedro,

Thank you for posting to the forum!

At first glance I’m not seeing any clear hints to what the issue is. To help with the debugging, can you provide some information about your system and how you installed ASPECT/deal.II?

Thanks!
John

3

Thanks for your reply.

My operating system is MacOs BigSur. I installed deal.II by downloading the prepackaged .dmg file from the download page and dragging the deal.II.app to the applications folder. Specifically, I downloaded dealii-9.3.0-bigsur-intel.dmg, available in deal.II Downloads.

To install aspect in my users directory in the optimized mode, I did the following steps (always within the deal.II terminal):

git clone https://github.com/geodynamics/aspect.git

mkdir ~/aspect/release

cd ~/aspect/release

cmake ~/aspect

make release

make

All of this seemed to work well. However, when I tried make test or to run a .prm file, I get the error I pasted in my previous message.

4

Hi Pedro,

Yes, at first glance I don’t see anything wrong with your workflow.

Question 1 - if you compile in Debug mode (i.e, don’t do make release), does everything work properly?

Question 2 - In release mode, can you run a model with ~/aspect/release/.aspect prm_file_name.prm?

Can you also report the version of Xcode you have installed? This has caused problems in the past.

Cheers,
John

5

I bet that this is the problem. The dmg package is built for a specific
processor architecture, and while operating systems running on a different
processor will gladly install the DMG, it may not run if, for example, you
have an older processor than the one Luca used when building the dmg package.

I’m not a Mac person, so don’t know the workflow well. But I think that the
only option you have is to build deal.II yourself on your machine, for example
using the ‘candi’ script.

Best
W.

6

Hello!

The computer has the new M1 processor, so that could be the problem.

I think that candi only works for linux systems. Could I use another alternative software to build deal.II like Spack?

Thanks!

Pedro

7

Answer to question 1: It doesn’t work in Debug mode either.

Answer to question 2: I haven’t tried to run a model in release mode without using mpirun as you say. I’ll try it on monday.

The version of Xcode I have installed is the latest version (version 12.5.1).

I will keep trying to solve the problem.

Thank you very much

Pedro

8

Hi Pedro,

The computer has the new M1 processor, so that could be the problem.

Yes, that is definitely the issue :slight_smile:

Here the instructions (quite new) for compiling on the M1 processor, which Timo Heister kindly put together at the last hackathon:

Let us know how it goes!
John

9

Hello!

I have followed Timo’s instructions for compiling on the M1 processor but I get an error when I try to install deal.22. Specifically, when I type:

./candi.sh -j 8 --packages=“hdf5 p4est trilinos dealii”

within the candi directory, I get the following error message:

[ 90%] Building CXX object examples/CMakeFiles/step-16b.release.dir/step-16b/step-16b.cc.o

[ 90%] Linking CXX executable …/bin/step-22.release

[ 90%] Linking CXX executable …/bin/step-56.release

[ 90%] Built target step-22.release

[ 90%] Building CXX object examples/CMakeFiles/step-74.release.dir/step-74/step-74.cc.o

[ 90%] Built target step-56.release

[ 90%] Building CXX object examples/CMakeFiles/step-39.release.dir/step-39/step-39.cc.o

[ 90%] Linking CXX executable …/bin/step-76.release

[ 90%] Built target step-76.release

[ 90%] Building CXX object examples/CMakeFiles/step-34.release.dir/step-34/step-34.cc.o

[ 90%] Linking CXX executable …/bin/step-11.release

[ 90%] Built target step-11.release

[ 90%] Building CXX object examples/CMakeFiles/step-15.release.dir/step-15/step-15.cc.o

[ 90%] Linking CXX executable …/bin/step-47.release

[ 90%] Built target step-47.release

[ 91%] Building CXX object examples/CMakeFiles/step-40.release.dir/step-40/step-40.cc.o

[ 91%] Linking CXX executable …/bin/step-14.release

[ 91%] Built target step-14.release

[ 91%] Building CXX object examples/CMakeFiles/step-1.release.dir/step-1/step-1.cc.o

[ 91%] Linking CXX executable …/bin/step-21.release

[ 91%] Linking CXX executable …/bin/step-74.release

[ 91%] Built target step-21.release

[ 91%] Building CXX object examples/CMakeFiles/step-4.release.dir/step-4/step-4.cc.o

[ 91%] Built target step-74.release

[ 91%] Building CXX object examples/CMakeFiles/step-20.release.dir/step-20/step-20.cc.o

[ 91%] Linking CXX executable …/bin/step-1.release

[ 91%] Built target step-1.release

[ 91%] Building CXX object examples/CMakeFiles/step-7.release.dir/step-7/step-7.cc.o

[ 91%] Linking CXX executable …/bin/step-40.release

[ 91%] Linking CXX executable …/bin/step-15.release

[ 91%] Built target step-40.release

[ 91%] Building CXX object examples/CMakeFiles/step-43.release.dir/step-43/step-43.cc.o

[ 91%] Built target step-15.release

[ 91%] Building CXX object examples/CMakeFiles/step-10.release.dir/step-10/step-10.cc.o

[ 91%] Linking CXX executable …/bin/step-16b.release

[ 91%] Built target step-16b.release

[ 91%] Building CXX object examples/CMakeFiles/step-52.release.dir/step-52/step-52.cc.o

[ 91%] Linking CXX executable …/bin/step-39.release

[ 91%] Linking CXX executable …/bin/step-34.release

[ 91%] Built target step-39.release

[ 91%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o

[ 91%] Linking CXX shared library …/lib/libdeal_II.g.dylib

[ 91%] Built target step-34.release

[ 91%] Linking CXX executable …/bin/step-10.release

[ 91%] Linking CXX executable …/bin/step-4.release

[ 91%] Built target step-10.release

[ 91%] Built target step-4.release

[ 91%] Linking CXX executable …/bin/step-20.release

[ 91%] Linking CXX executable …/bin/step-52.release

[ 91%] Built target step-20.release

[ 91%] Built target step-52.release

[ 91%] Linking CXX executable …/bin/step-7.release

[ 91%] Built target step-7.release

[ 91%] Linking CXX executable …/bin/step-43.release

[ 91%] Built target step-43.release

final section layout:

__TEXT/__text addr=0x00018BA0, size=0x07A0B2E0, fileOffset=0x00018BA0, type=1

__TEXT/__stubs addr=0x07A23E80, size=0x00650124, fileOffset=0x07A23E80, type=29

__TEXT/__stub_helper addr=0x08073FA4, size=0x00002124, fileOffset=0x08073FA4, type=33

__TEXT/__const addr=0x080760D0, size=0x002B6E58, fileOffset=0x080760D0, type=0

__TEXT/__cstring addr=0x0832CF28, size=0x01739C38, fileOffset=0x0832CF28, type=13

__TEXT/__eh_frame addr=0x09A66B60, size=0x024E14A0, fileOffset=0x09A66B60, type=19

__DATA_CONST/__got addr=0x0BF48000, size=0x000353C0, fileOffset=0x0BF48000, type=30

__DATA_CONST/__mod_init_func addr=0x0BF7D3C0, size=0x00000C00, fileOffset=0x0BF7D3C0, type=34

__DATA_CONST/__const addr=0x0BF7DFC0, size=0x00134100, fileOffset=0x0BF7DFC0, type=0

__DATA/__la_symbol_ptr addr=0x0C0B4000, size=0x00435618, fileOffset=0x0C0B4000, type=28

__DATA/__gcc_except_tab addr=0x0C4E9618, size=0x005FF1F0, fileOffset=0x0C4E9618, type=0

__DATA/__data addr=0x0CAE8808, size=0x0000AEA8, fileOffset=0x0CAE8808, type=0

__DATA/__bss addr=0x0CAF36B0, size=0x00009C49, fileOffset=0x00000000, type=26

__DATA/__common addr=0x0CAFD300, size=0x00000719, fileOffset=0x00000000, type=26

ld: b(l) ARM64 branch out of range (134586840 max is +/-128MB): from _ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4 (0x00018C58) to ___assert_rtn@0x00000000 (0x08073344) in ‘_ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4’ from …/bundled/boost-1.70.0/libs/serialization/src/CMakeFiles/obj_boost_serialization_debug.dir/archive_exception.cpp.o for architecture arm64

collect2: error: ld returned 1 exit status

make[2]: *** [lib/libdeal_II.g.9.3.1.dylib] Error 1

make[2]: *** Deleting file `lib/libdeal_II.g.9.3.1.dylib’

make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2

make: *** [all] Error 2

Failure with exit status: 2

Exit message: There was a problem building dealii v9.3.1.

Any idea what the problem might be?

Thanks, Pedro

10

Hi Pedro,

I’m not sure what the fix is for that error, this may be very compiler and architecture specific:
ld: b(l) ARM64 branch out of range (134586840 max is +/-128MB): from _ *ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4* (0x00018C58) to ___assert_rtn@0x00000000 (0x08073344) in ‘_ *ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4* ’ from …/bundled/boost-1.70.0/libs/serialization/src/CMakeFiles/obj_boost_serialization_debug.dir/archive_exception.cpp.o for architecture arm64

What you can try doing is not rerunning Candi and not have the deal.II examples built. I believe you can do this in candi.cfg by setting BUILD_EXAMPLES=OFF.

Alternatively, setting the following variable in candi.cfg should also work:
DEAL_CONFOPTS="-DDEAL_II_COMPONENT_EXAMPLES:BOOL=OFF"

Unfortunately the deal.II build failed before getting to step-32, which is the most relevant one for ASPECT. You will need to build ASPECT run the test suite set to make sure nothing is off. Please let us know how this goes!

FYI, you may get a large number of failing tests, but the key is whether they are simply very small changes to already small values, or significant changes to the test results. The test results are machine/compiler dependent to a small degree, but this will be the case for all codes.

Cheers,
John

11

I have not seen this error before. John is right in that the examples are not crucial, but ASPECT might fail the same way. We will see.

Can you please post your detailed.log? It should be inside the destination folder then tmp/build/deal.II/. Maybe that tells me what is different on your system.

12

I have set BUILD_EXAMPLES=OFF and run Candi again. Now, it reaches 100 % but at the end I get the same error:

[ 98%] Building CXX object source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qp.cc.o
[100%] Building CXX object source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
[100%] Built target obj_fe_debug
[100%] Built target obj_numerics_debug
[100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o
[100%] Linking CXX shared library …/lib/libdeal_II.g.dylib
final section layout:
__TEXT/__text addr=0x00018BA0, size=0x07A0B2E0, fileOffset=0x00018BA0, type=1
__TEXT/__stubs addr=0x07A23E80, size=0x00650124, fileOffset=0x07A23E80, type=29
__TEXT/__stub_helper addr=0x08073FA4, size=0x00002124, fileOffset=0x08073FA4, type=33
__TEXT/__const addr=0x080760D0, size=0x002B6E58, fileOffset=0x080760D0, type=0
__TEXT/__cstring addr=0x0832CF28, size=0x01739C38, fileOffset=0x0832CF28, type=13
__TEXT/__eh_frame addr=0x09A66B60, size=0x024E14A0, fileOffset=0x09A66B60, type=19
__DATA_CONST/__got addr=0x0BF48000, size=0x000353C0, fileOffset=0x0BF48000, type=30
__DATA_CONST/__mod_init_func addr=0x0BF7D3C0, size=0x00000C00, fileOffset=0x0BF7D3C0, type=34
__DATA_CONST/__const addr=0x0BF7DFC0, size=0x00134100, fileOffset=0x0BF7DFC0, type=0
__DATA/__la_symbol_ptr addr=0x0C0B4000, size=0x00435618, fileOffset=0x0C0B4000, type=28
__DATA/__gcc_except_tab addr=0x0C4E9618, size=0x005FF1F0, fileOffset=0x0C4E9618, type=0
__DATA/__data addr=0x0CAE8808, size=0x0000AEA8, fileOffset=0x0CAE8808, type=0
__DATA/__bss addr=0x0CAF36B0, size=0x00009C49, fileOffset=0x00000000, type=26
__DATA/__common addr=0x0CAFD300, size=0x00000719, fileOffset=0x00000000, type=26
ld: b(l) ARM64 branch out of range (134586840 max is +/-128MB): from _ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4 (0x00018C58) to ___assert_rtn@0x00000000 (0x08073344) in ‘_ZN5boost7archive17archive_exceptionC2ENS1_14exception_codeEPKcS4’ from …/bundled/boost-1.70.0/libs/serialization/src/CMakeFiles/obj_boost_serialization_debug.dir/archive_exception.cpp.o for architecture arm64
collect2: error: ld returned 1 exit status
make[2]: *** [lib/libdeal_II.g.9.3.1.dylib] Error 1
make[2]: *** Deleting file `lib/libdeal_II.g.9.3.1.dylib’
make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building dealii v9.3.1.

13

Here is the detailed.log:

deal.II configuration:

CMAKE_BUILD_TYPE: DebugRelease

BUILD_SHARED_LIBS: ON

CMAKE_INSTALL_PREFIX: /Users/pedro_gea/dealii-candi/deal.II-v9.3.1

CMAKE_SOURCE_DIR: /Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1

(version 9.3.1, shortrev 7f0732c521)

CMAKE_BINARY_DIR: /Users/pedro_gea/dealii-candi/tmp/build/deal.II-v9.3.1

CMAKE_CXX_COMPILER: GNU 11.1.0 on platform Darwin arm64

/opt/homebrew/bin/mpicxx

C++ language standard: C++17

CMAKE_C_COMPILER: /opt/homebrew/bin/mpicc

CMAKE_Fortran_COMPILER: /opt/homebrew/bin/mpifort

CMAKE_GENERATOR: Unix Makefiles

Base configuration (prior to feature configuration):

DEAL_II_CXX_FLAGS: -pedantic -fPIC -Wall -Wextra -Wmissing-braces -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -Wno-class-memaccess -fopenmp-simd -ftemplate-depth=1024

DEAL_II_CXX_FLAGS_RELEASE: -O2 -funroll-loops -funroll-all-loops -fstrict-aliasing -Wno-unused-local-typedefs

DEAL_II_CXX_FLAGS_DEBUG: -O0 -ggdb

DEAL_II_LINKER_FLAGS: -fuse-ld=lld

DEAL_II_LINKER_FLAGS_RELEASE:

DEAL_II_LINKER_FLAGS_DEBUG: -ggdb

DEAL_II_DEFINITIONS:

DEAL_II_DEFINITIONS_RELEASE:

DEAL_II_DEFINITIONS_DEBUG: DEBUG

DEAL_II_USER_DEFINITIONS:

DEAL_II_USER_DEFINITIONS_REL:

DEAL_II_USER_DEFINITIONS_DEB: DEBUG

DEAL_II_INCLUDE_DIRS

DEAL_II_USER_INCLUDE_DIRS:

DEAL_II_BUNDLED_INCLUDE_DIRS:

DEAL_II_LIBRARIES:

DEAL_II_LIBRARIES_RELEASE:

DEAL_II_LIBRARIES_DEBUG:

DEAL_II_VECTORIZATION_WIDTH_IN_BITS: 0

DEAL_II_HAVE_CXX17

Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON):

( DEAL_II_WITH_64BIT_INDICES = OFF )

( DEAL_II_WITH_ADOLC = OFF )

( DEAL_II_WITH_ARBORX = OFF )

( DEAL_II_WITH_ARPACK = OFF )

( DEAL_II_WITH_ASSIMP = OFF )

DEAL_II_WITH_BOOST set up with bundled packages

BOOST_CXX_FLAGS = -Wno-unused-local-typedefs

BOOST_DEFINITIONS = BOOST_NO_AUTO_PTR

BOOST_USER_DEFINITIONS = BOOST_NO_AUTO_PTR

BOOST_BUNDLED_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1/bundled/boost-1.70.0/include

DEAL_II_WITH_COMPLEX_VALUES = ON

( DEAL_II_WITH_CUDA = OFF )

( DEAL_II_WITH_GINKGO = OFF )

( DEAL_II_WITH_GMSH = OFF )

( DEAL_II_WITH_GSL = OFF )

DEAL_II_WITH_HDF5 set up with external dependencies

HDF5_DIR = /Users/pedro_gea/dealii-candi/hdf5-1.10.7

HDF5_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/hdf5-1.10.7/include

HDF5_USER_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/hdf5-1.10.7/include

HDF5_LIBRARIES = /Users/pedro_gea/dealii-candi/hdf5-1.10.7/lib/libhdf5_hl.dylib;/Users/pedro_gea/dealii-candi/hdf5-1.10.7/lib/libhdf5.dylib

DEAL_II_WITH_KOKKOS set up with external dependencies

DEAL_II_WITH_LAPACK set up with external dependencies

LAPACK_WITH_64BIT_BLAS_INDICES = OFF

LAPACK_LINKER_FLAGS =

LAPACK_INCLUDE_DIRS =

LAPACK_USER_INCLUDE_DIRS =

LAPACK_LIBRARIES = -lm;-ldl;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/Accelerate.framework

( DEAL_II_WITH_METIS = OFF )

DEAL_II_WITH_MPI set up with external dependencies

MPI_VERSION = 3.1

MPI_C_COMPILER = /opt/homebrew/bin/mpicc

MPI_CXX_COMPILER = /opt/homebrew/bin/mpicxx

MPI_Fortran_COMPILER = /opt/homebrew/bin/mpifort

MPI_CXX_FLAGS =

MPI_LINKER_FLAGS =

MPI_INCLUDE_DIRS =

MPI_USER_INCLUDE_DIRS =

DEAL_II_WITH_MUPARSER set up with bundled packages

MUPARSER_BUNDLED_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1/bundled/muparser_v2_2_4//include

( DEAL_II_WITH_OPENCASCADE = OFF )

DEAL_II_WITH_P4EST set up with external dependencies

P4EST_VERSION = 2.2

P4EST_DIR = /Users/pedro_gea/dealii-candi/p4est-2.2

P4EST_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/p4est-2.2/FAST/include

P4EST_USER_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/p4est-2.2/FAST/include

P4EST_LIBRARIES = optimized;/Users/pedro_gea/dealii-candi/p4est-2.2/FAST/lib/libp4est.dylib;/Users/pedro_gea/dealii-candi/p4est-2.2/FAST/lib/libsc.dylib;debug;/Users/pedro_gea/dealii-candi/p4est-2.2/DEBUG/lib/libp4est.dylib;/Users/pedro_gea/dealii-candi/p4est-2.2/DEBUG/lib/libsc.dylib;general;-lm;-ldl;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.3.sdk/System/Library/Frameworks/Accelerate.framework

( DEAL_II_WITH_PETSC = OFF )

( DEAL_II_WITH_SCALAPACK = OFF )

( DEAL_II_WITH_SLEPC = OFF )

( DEAL_II_WITH_SUNDIALS = OFF )

( DEAL_II_WITH_SYMENGINE = OFF )

DEAL_II_WITH_TBB set up with bundled packages

TBB_CXX_FLAGS = -Wno-parentheses

TBB_BUNDLED_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1/bundled/tbb-2018_U2/include

DEAL_II_WITH_TRILINOS set up with external dependencies

TRILINOS_VERSION = 12.18.1

TRILINOS_DIR = /Users/pedro_gea/dealii-candi/trilinos-release-12-18-1

TRILINOS_LINKER_FLAGS =

TRILINOS_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/include

TRILINOS_USER_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/include

TRILINOS_LIBRARIES = /Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/librol.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtempus.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libmuelu-adapters.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libmuelu-interface.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libmuelu.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/liblocathyra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/liblocaepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/liblocalapack.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libloca.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libnoxepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libnoxlapack.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libnox.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libintrepid2.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libintrepid.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libteko.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikos.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosbelos.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosamesos2.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosaztecoo.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosamesos.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosml.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libstratimikosifpack.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libanasazitpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libModeLaplace.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libanasaziepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libanasazi.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libamesos2.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libshylu_nodetacho.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libbelosxpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libbelostpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libbelosepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libbelos.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libml.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libifpack.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libzoltan2.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libpamgen_extras.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libpamgen.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libamesos.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libgaleri-xpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libgaleri-epetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libaztecoo.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libisorropia.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libxpetra-sup.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libxpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libthyratpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libthyraepetraext.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libthyraepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libthyracore.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtrilinosss.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetraext.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetrainout.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libkokkostsqr.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetraclassiclinalg.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetraclassicnodeapi.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtpetraclassic.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libepetraext.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libtriutils.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libshards.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libzoltan.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libepetra.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/libsacado.dylib;/Users/pedro_gea/dealii-candi/trilinos-release-12-18-1/lib/librtop.dylib;/Users/pedro_gea/dealii-candi/trili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DEAL_II_WITH_UMFPACK set up with bundled packages

UMFPACK_BUNDLED_INCLUDE_DIRS = /Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1/bundled/umfpack/UMFPACK/Include;/Users/pedro_gea/dealii-candi/tmp/unpack/deal.II-v9.3.1/bundled/umfpack/AMD/Include

DEAL_II_WITH_ZLIB set up with external dependencies

ZLIB_VERSION = 1.2.11

ZLIB_INCLUDE_DIRS = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.3.sdk/usr/include

ZLIB_LIBRARIES = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.3.sdk/usr/lib/libz.tbd

Component configuration:

( DEAL_II_COMPONENT_DOCUMENTATION = OFF )

( DEAL_II_COMPONENT_EXAMPLES = OFF )

( DEAL_II_COMPONENT_PACKAGE = OFF )

( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )

14

Thank you. I will need to try to reproduce on my system to fix this. Can I ask you to try the following?
edit candi.cfg to say

DEAL_II_CONFOPTS="-DDEAL_II_WITH_COMPLEX_VALUES=OFF -DDEAL_II_CXX_FLAGS_DEBUG='-Os' -DDEAL_II_COMPONENT_EXAMPLES=OFF"

then delete tmp/build/deal.II-v9.3.1
and run again? This might reduce the library size so that you are able to link.

Best,
Timo

15

Hello! That worked! Deal.II has been installed successfully.

However, when I type make to compile ASPECT, I get the following error:

[ 67%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_39_cxx.cxx.o

[ 68%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_35_cxx.cxx.o

[ 69%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_38_cxx.cxx.o

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_36_cxx.cxx.o] Error 1

make[2]: *** Waiting for unfinished jobs…

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_34_cxx.cxx.o] Error 1

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_40_cxx.cxx.o] Error 1

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_39_cxx.cxx.o] Error 1

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

g+±11: error: unrecognized command-line option ’ -Xarch_arm64 ’

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_38_cxx.cxx.o] Error 1

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_37_cxx.cxx.o] Error 1

make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_35_cxx.cxx.o] Error 1

make[1]: *** [CMakeFiles/aspect.dir/all] Error 2

make: *** [all] Error 2

I guess the problem is in the computer architecture again but I have not been able to solve it. Any ideas for this?

Here is the detailed.log in case it would be helpful:

ASPECT configuration:

ASPECT_VERSION: 2.4.0-pre

GIT REVISION: 4dacd248b (master)

CMAKE_BUILD_TYPE: Release

DEAL_II_DIR: /Users/pedro_gea/dealii-candi/deal.II-v9.3.1/lib/cmake/deal.II

DEAL_II VERSION: 9.3.1

ASPECT_USE_FP_EXCEPTIONS: OFF

ASPECT_RUN_ALL_TESTS: OFF

ASPECT_USE_SHARED_LIBS: ON

ASPECT_HAVE_LINK_H: OFF

ASPECT_WITH_LIBDAP: OFF

ASPECT_WITH_WORLD_BUILDER: ON /Users/pedro_gea/aspect/contrib/world_builder

ASPECT_PRECOMPILE_HEADERS: ON

ASPECT_UNITY_BUILD: ON

CMAKE_INSTALL_PREFIX: /usr/local

CMAKE_SOURCE_DIR: /Users/pedro_gea/aspect

CMAKE_BINARY_DIR: /Users/pedro_gea/aspect/release

CMAKE_CXX_COMPILER: GNU 11.1.0 on platform Darwin arm64

/opt/homebrew/bin/mpicxx

PARAMETER_GUI_EXECUTABLE: PARAMETER_GUI_EXECUTABLE-NOTFOUND

LINKAGE: DYNAMIC

COMPILE_FLAGS:

_WITH_CXX14: ON

_WITH_CXX17: TRUE

_MPI_VERSION: 3.1

_WITH_64BIT_INDICES: OFF

Thank you very much again,

Pedro

16

Very weird, I apologize. M1 is still very new and I haven’t seen these problems on my test system.

Are you compiling ASPECT and deal.II in a native terminal window (not the x64 terminal)? Can you try specifying

cmake -D ASPECT_PRECOMPILE_HEADERS=OFF -D ASPECT_UNITY_BUILD=OFF .

in your ASPECT build directory? Maybe these settings mess up your build.
If that does not work, can you show me the output for

make VERBOSE=ON

That should show the compiler invocation.

17

No worries, I am very grateful for all your help.

I am working in the native terminal. I have typed

cmake -D ASPECT_PRECOMPILE_HEADERS=OFF -D ASPECT_UNITY_BUILD=OFF .

in the ASPECT directory and it seems that the previous error has been fixed. However, I get another different error when the aspect executable is being linked. The message I get is as follows:

[ 98%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/utilities.cc.o
[ 98%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/world.cc.o
[ 98%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/wrapper_c.cc.o
[100%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/wrapper_cpp.cc.o
[100%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/parameters.cc.o
[100%] Linking CXX executable aspect
duplicate symbol ‘__ZTSN6aspect13GeometryModel8internal13ChunkGeometryILi3EEE’ in:
CMakeFiles/aspect.dir/source/geometry_model/chunk.cc.o
CMakeFiles/aspect.dir/source/geometry_model/two_merged_chunks.cc.o
duplicate symbol ‘__ZTIN6aspect13GeometryModel8internal13ChunkGeometryILi3EEE’ in:
CMakeFiles/aspect.dir/source/geometry_model/chunk.cc.o
CMakeFiles/aspect.dir/source/geometry_model/two_merged_chunks.cc.o
duplicate symbol ‘__ZTSN6aspect13GeometryModel8internal13ChunkGeometryILi2EEE’ in:
CMakeFiles/aspect.dir/source/geometry_model/chunk.cc.o
CMakeFiles/aspect.dir/source/geometry_model/two_merged_chunks.cc.o
duplicate symbol ‘__ZTIN6aspect13GeometryModel8internal13ChunkGeometryILi2EEE’ in:
CMakeFiles/aspect.dir/source/geometry_model/chunk.cc.o
CMakeFiles/aspect.dir/source/geometry_model/two_merged_chunks.cc.o
ld: 4 duplicate symbols for architecture arm64
collect2: error: ld returned 1 exit status
make[2]: *** [aspect] Error 1
make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
make: *** [all] Error 2

I have tried to build ASPECT in both debug mode and release mode and in both cases I get the same error. I have tried to remove the duplicate symbols ‘__ZTSN6aspect13GeometryModel8internal13ChunkGeometryILi3EEE’ from chunk.cc.o and two_merged_chunks.cc.o but it does not work.

Have you seen this error before? How could I fix it?

Pedro

18

This is indeed a bug in ASPECT. I have a fix here: remove duplicate ChunkGeometry instantiation by tjhei · Pull Request #4351 · geodynamics/aspect · GitHub
You can try it yourself (or wait until it is merged and then update). Let me know if this works and if there are other problems.

19

It worked.

Thank you very much for your patience!

Best,
Pedro