[Users] sim build problems
Erik Schnetter
schnetter at gmail.com
Thu Mar 24 12:15:07 CDT 2022
Lorenzo
As a side remark:
"gcc" on macOS is actually a version of "clang". This version has been
modified by Apple to remove support for OpenMP. There are work-around
for using OpenMP with Apple's clang, or you can configure Cactus
without OpenMP. The recommended solution is to install gcc instead,
following Roland's pointers.
-erik
On Thu, Mar 24, 2022 at 10:30 AM Roland Haas <rhaas at illinois.edu> wrote:
>
> Hello Lorenzo,
>
> Thank you for your email.
>
> Looking at the errors and the fact that it used the clang compiler I
> would suspect that the issue is with using clang.
>
> We document how to use gcc on macOS and I would suggest you try this
> first.
>
> You can find instructions at the top of the "New user tutorial"
> notebook:
>
> https://github.com/nds-org/jupyter-et/blob/master/tutorial-server/notebooks/CactusTutorial.ipynb
>
> in the "Prerequisites" section.
>
> --8<--
>
> On Mac, please first
>
> Install Xcode from the Apple App Store. In addition agree to Xcode license and install the Xcode Command Line Tools in Terminal
>
> sudo xcodebuild -license
> sudo xcode-select --install
>
> when using MacPorts
> install MacPorts for your version of the Mac operating system, if you have not already installed it (https://www.macports.org/install.php).
> Next, please install the following packages, using the commands:
>
> sudo port -N install pkgconfig gcc11 openmpi-gcc11 fftw-3 gsl jpeg zlib openssl zlib bash subversion ld64
> # required of macOS Monterey, see https://gcc.gnu.org/bugzilla/show_bug.cgi?id=102992
> sudo port -N install hdf5 +fortran +gcc11 +openmpi configure.env="GFORTRAN_UNBUFFERED_ALL=1"
> sudo port select mpi openmpi-gcc11-fortran
> sudo port select gcc mp-gcc11
>
> when using HomeBrew
> install HomeBrew for your version of the Mac operating system, if you have not already installed it (https://brew.sh/).
> Next, please install the following packages, using the commands:
>
> brew install fftw gcc gsl hdf5 hwloc jpeg open-mpi openssl zlib pkg-config bash subversion
> --8<--
>
> Yours,
> Roland
>
> > Hi,
> > I'm trying to build the EinsteinToolkit running the command:
> >
> > ./simfactory/bin/sim build -j2 --thornlist ../einsteintoolkit.th.
> >
> > on my mac but the result, after nearly 1h, is the following:
> >
> > Undefined symbols for architecture x86_64:
> >
> > "_GOMP_loop_nonmonotonic_dynamic_next", referenced from:
> >
> >
> > __ZNK13CarpetInterp219fasterp_setup_gen_tINS_17fasterp_src_loc_tEE11interpolateEPK4_cGHRKSt6vectorIiSaIiEERS6_IPdSaISB_EE._omp_fn.0
> > in fasterp.cc.o
> >
> >
> > __ZNK13CarpetInterp219fasterp_setup_gen_tINS_22fasterp_eno2_src_loc_tEE11interpolateEPK4_cGHRKSt6vectorIiSaIiEERS6_IPdSaISB_EE._omp_fn.0
> > in fasterp.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIfEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIdEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIeEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> > _SetMatrix_JFD._omp_fn.0 in FuncAndJacobian.c.o
> >
> > _J_times_dv._omp_fn.0 in FuncAndJacobian.c.o
> >
> > ...
> >
> > "_GOMP_loop_nonmonotonic_dynamic_start", referenced from:
> >
> >
> > __ZNK13CarpetInterp219fasterp_setup_gen_tINS_17fasterp_src_loc_tEE11interpolateEPK4_cGHRKSt6vectorIiSaIiEERS6_IPdSaISB_EE._omp_fn.0
> > in fasterp.cc.o
> >
> >
> > __ZNK13CarpetInterp219fasterp_setup_gen_tINS_22fasterp_eno2_src_loc_tEE11interpolateEPK4_cGHRKSt6vectorIiSaIiEERS6_IPdSaISB_EE._omp_fn.0
> > in fasterp.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIfEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIdEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> >
> > __ZN10NaNChecker10CHECK_DATAIeEEvPKT_iPKdPKNS_17t_nanchecker_infoERiiiiiPKS5_PKcRK16GROUPDYNAMICDATAi._omp_fn.0
> > in NaNCheck.cc.o
> >
> > _SetMatrix_JFD._omp_fn.0 in FuncAndJacobian.c.o
> >
> > _J_times_dv._omp_fn.0 in FuncAndJacobian.c.o
> >
> > ...
> >
> > "_GOMP_loop_nonmonotonic_guided_next", referenced from:
> >
> > ___noexcision_mod_MOD_multiply._omp_fn.0 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.0 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.1 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.2 in NoExcision_mod.F90.o
> >
> > "_GOMP_loop_nonmonotonic_guided_start", referenced from:
> >
> > ___noexcision_mod_MOD_multiply._omp_fn.0 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.0 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.1 in NoExcision_mod.F90.o
> >
> > ___noexcision_mod_MOD_residual._omp_fn.2 in NoExcision_mod.F90.o
> >
> > "_GOMP_parallel", referenced from:
> >
> > _ADMDerivatives_CalcDerivatives in calc_derivs.cc.o
> >
> > _Baikal_zero_rhss in zero_rhss.c.o
> >
> > _Baikal_floor_the_lapse in floor_the_lapse.c.o
> >
> > _Baikal_ADM_to_BSSN in ADM_to_BSSN.c.o
> >
> > _Baikal_BSSN_to_ADM in BSSN_to_ADM.c.o
> >
> > _Baikal_BSSN_Ricci_FD_order_2 in BSSN_Ricci_FD_order_2.c.o
> >
> > _Baikal_BSSN_Ricci_FD_order_4 in BSSN_Ricci_FD_order_4.c.o
> >
> > ...
> >
> > "__gfortran_os_error_at", referenced from:
> >
> > _ahfinder_ in AHFinder.F.o
> >
> > _ahfinder_dis_ in AHFinder_dis.F.o
> >
> > _ahfinder_int_ in AHFinder_int.F.o
> >
> > _linmin_ in AHFinder_pow.F.o
> >
> > _ahfinder_initguess_ in AHFinder_initguess.F.o
> >
> > _ahfinder_gau_ in AHFinder_gau.F.o
> >
> > ___carpet_boxtypes_MOD_splitregionsrecursive in carpet_boxtypes.F90.o
> >
> > ...
> >
> > ld: symbol(s) not found for architecture x86_64
> >
> > collect2: error: ld returned 1 exit status
> >
> > make[1]: *** [/Users/lorenzo/Cactus/exe/cactus_sim] Error 1
> >
> > make: *** [sim] Error 2
> >
> >
> > Is there a way to make it work?
> >
> >
> > I'm using a macbook air (2017) with macOs monterey 12.3 and xcode 13.3.
> >
> >
> > the gcc version is the following:
> >
> >
> > Apple clang version 13.1.6 (clang-1316.0.21.2)
> >
> > Target: x86_64-apple-darwin21.4.0
> >
> > Thread model: posix
> >
> > InstalledDir:
> > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> >
> >
> > Best regards,
> >
> > Lorenzo.
>
>
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://keys.gnupg.net.
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--
Erik Schnetter <schnetter at gmail.com>
http://www.perimeterinstitute.ca/personal/eschnetter/
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