[mesa-users] /Mesa/mesa-r7503/mtx/test FAILED. gfortran.exec error.

Manser, Christopher C.Manser at warwick.ac.uk
Tue Apr 21 09:29:38 EDT 2015


I have these lines in my .bashrc / .bash_profile

export MESASDK_ROOT=/Applications/mesasdk
source $MESASDK_ROOT/bin/mesasdk_init.sh

As far as I am aware I haven't done anything to effect these.

I just go straight to the MESA_DIR and sudo ./install

________________________________________
From: Richard Townsend <townsend at astro.wisc.edu>
Sent: 21 April 2015 14:24
To: Manser, Christopher
Cc: mesa-users at lists.sourceforge.net
Subject: Re: [mesa-users] /Mesa/mesa-r7503/mtx/test FAILED. gfortran.exec error.

Ah yes, my fix won’t address how GYRE compiles.

We could also hack GYRE’s makefile system; but let’s instead try to figure out what exactly is going wrong. All of the symptoms point to MESASDK_ROOT becoming unset at some point during the compilation process. But I’m puzzled as to how that might happen. You don’t unset it at any point, do you?

> On Apr 20, 2015, at 4:06 PM, Manser, Christopher <C.Manser at warwick.ac.uk> wrote:
>
> Sorry I didn't see the new update, added the new bit but still fails when doing the gyre package.
>
> ________________________________________
> From: Manser, Christopher <C.Manser at warwick.ac.uk>
> Sent: 20 April 2015 18:41
> To: Richard Townsend
> Cc: mesa-users at lists.sourceforge.net
> Subject: Re: [mesa-users] /Mesa/mesa-r7503/mtx/test FAILED. gfortran.exec error.
>
> Okay, I have set the section in the makefile_header as:
>
> LOAD_LAPACK = /Applications/mesasdk/lib/liblapack.a
> LOAD_BLAS = /Applications/mesasdk/lib/libxblas.a /Applications/mesasdk/lib/libblas.a
>
> Which seems to give the same error:
>
> __________________________________________
>
>
> ************************************************
>
> /Mesa/mesa-r7503/star
> building star package.
>
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero -fopenmp  -o ../star \
>        run_star_extras.o run_star.o  run.o -L../../make -lstar -L../../../lib -lionization -latm -lcolors -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu /Applications/mesasdk/lib/liblapack.a /Applications/mesasdk/lib/libxblas.a /Applications/mesasdk/lib/libblas.a `mesasdk_pgplot_link` `mesasdk_se_link`
> ld: warning: directory not found for option '-L/lib'
> ld: warning: directory not found for option '-L/lib'
> ld: warning: directory not found for option '-L/lib'
> export
> done
>
> mesa/star has been built, tested, and exported.
>
> ************************************************
>
> /Mesa/mesa-r7503/gyre
> building gyre package.
>
> make: `libgyre.a' is up to date.
> make: `libgyre.a' is up to date.
> gfortran -fopenmp -o ../tester test_gyre.o -L../../make -lgyre /Applications/mesasdk/lib/liblapack.a -L../../../lib -lconst
> Undefined symbols for architecture x86_64:
>  "_daxpy_", referenced from:
>      _dgehrd_ in liblapack.a(dgehrd.o)
>      _dtrevc_ in liblapack.a(dtrevc.o)
>      _dlahr2_ in liblapack.a(dlahr2.o)
>  "_dcopy_", referenced from:
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dtrevc_ in liblapack.a(dtrevc.o)
>      _dlahqr_ in liblapack.a(dlahqr.o)
>      _dlahr2_ in liblapack.a(dlahr2.o)
>      _dlarfb_ in liblapack.a(dlarfb.o)
>      _dlaqr3_ in liblapack.a(dlaqr3.o)
>      _dlaqr2_ in liblapack.a(dlaqr2.o)
>      ...
>  "_ddot_", referenced from:
>      _dtrevc_ in liblapack.a(dtrevc.o)
>  "_dgemm_", referenced from:
>      ___gyre_sysmtx_MOD_factorize_slu_r_._omp_fn.1 in libgyre.a(gyre_sysmtx.o)
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgetrf_ in liblapack.a(dgetrf.o)
>      _dgehrd_ in liblapack.a(dgehrd.o)
>      _dlahr2_ in liblapack.a(dlahr2.o)
>      _dlarfb_ in liblapack.a(dlarfb.o)
>      _dlaqr3_ in liblapack.a(dlaqr3.o)
>      ...
>  "_dgemv_", referenced from:
>      ___gyre_sysmtx_MOD_null_vector_slu_r_._omp_fn.0 in libgyre.a(gyre_sysmtx.o)
>      _dgbtrs_ in liblapack.a(dgbtrs.o)
>      _dtrevc_ in liblapack.a(dtrevc.o)
>      _dlahr2_ in liblapack.a(dlahr2.o)
>      _dlarf_ in liblapack.a(dlarf.o)
>      _dlarft_ in liblapack.a(dlarft.o)
>  "_dger_", referenced from:
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgbtrs_ in liblapack.a(dgbtrs.o)
>      _dgbtf2_ in liblapack.a(dgbtf2.o)
>      _dgetf2_ in liblapack.a(dgetf2.o)
>      _dlarf_ in liblapack.a(dlarf.o)
>  "_dnrm2_", referenced from:
>      _dgeev_ in liblapack.a(dgeev.o)
>      _dgebal_ in liblapack.a(dgebal.o)
>      _dlarfg_ in liblapack.a(dlarfg.o)
>  "_drot_", referenced from:
>      _dgeev_ in liblapack.a(dgeev.o)
>      _dlahqr_ in liblapack.a(dlahqr.o)
>      _dlaexc_ in liblapack.a(dlaexc.o)
>  "_dscal_", referenced from:
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgbtf2_ in liblapack.a(dgbtf2.o)
>      _dgeev_ in liblapack.a(dgeev.o)
>      _dgetf2_ in liblapack.a(dgetf2.o)
>      _dgebak_ in liblapack.a(dgebak.o)
>      _dgebal_ in liblapack.a(dgebal.o)
>      _dtrevc_ in liblapack.a(dtrevc.o)
>      ...
>  "_dswap_", referenced from:
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgbtrs_ in liblapack.a(dgbtrs.o)
>      _dgbtf2_ in liblapack.a(dgbtf2.o)
>      _dgetf2_ in liblapack.a(dgetf2.o)
>      _dgebak_ in liblapack.a(dgebak.o)
>      _dgebal_ in liblapack.a(dgebal.o)
>      _dlasy2_ in liblapack.a(dlasy2.o)
>      ...
>  "_dtbsv_", referenced from:
>      _dgbtrs_ in liblapack.a(dgbtrs.o)
>  "_dtrmm_", referenced from:
>      _dgehrd_ in liblapack.a(dgehrd.o)
>      _dlahr2_ in liblapack.a(dlahr2.o)
>      _dlarfb_ in liblapack.a(dlarfb.o)
>      _dlaqr5_ in liblapack.a(dlaqr5.o)
>  "_dtrmv_", referenced from:
>      _dlahr2_ in liblapack.a(dlahr2.o)
>      _dlarft_ in liblapack.a(dlarft.o)
>  "_dtrsm_", referenced from:
>      ___gyre_sysmtx_MOD_factorize_slu_r_._omp_fn.1 in libgyre.a(gyre_sysmtx.o)
>      ___gyre_sysmtx_MOD_null_vector_slu_r_.constprop.4 in libgyre.a(gyre_sysmtx.o)
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgetrf_ in liblapack.a(dgetrf.o)
>      _dgetrs_ in liblapack.a(dgetrs.o)
>  "_dzasum_", referenced from:
>      _ztrevc_ in liblapack.a(ztrevc.o)
>      _zlatrs_ in liblapack.a(zlatrs.o)
>  "_dznrm2_", referenced from:
>      _zgeev_ in liblapack.a(zgeev.o)
>      _zgebal_ in liblapack.a(zgebal.o)
>      _zlarfg_ in liblapack.a(zlarfg.o)
>  "_idamax_", referenced from:
>      _dgbtrf_ in liblapack.a(dgbtrf.o)
>      _dgbtf2_ in liblapack.a(dgbtf2.o)
>      _dgeev_ in liblapack.a(dgeev.o)
>      _dgetf2_ in liblapack.a(dgetf2.o)
>      _zgeev_ in liblapack.a(zgeev.o)
>      _dgebal_ in liblapack.a(dgebal.o)
>      _dtrevc_ in liblapack.a(dtrevc.o)
>      ...
>  "_izamax_", referenced from:
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgbtf2_ in liblapack.a(zgbtf2.o)
>      _zgetf2_ in liblapack.a(zgetf2.o)
>      _zgebal_ in liblapack.a(zgebal.o)
>      _ztrevc_ in liblapack.a(ztrevc.o)
>      _zlatrs_ in liblapack.a(zlatrs.o)
>  "_zaxpy_", referenced from:
>      _zgehrd_ in liblapack.a(zgehrd.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlatrs_ in liblapack.a(zlatrs.o)
>  "_zcopy_", referenced from:
>      ___gyre_magnus_ivp_MOD_solve_ in libgyre.a(gyre_magnus_ivp.o)
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zhseqr_ in liblapack.a(zhseqr.o)
>      _ztrevc_ in liblapack.a(ztrevc.o)
>      _zlahqr_ in liblapack.a(zlahqr.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlarfb_ in liblapack.a(zlarfb.o)
>      ...
>  "_zdotc_", referenced from:
>      _zlatrs_ in liblapack.a(zlatrs.o)
>  "_zdotu_", referenced from:
>      _zlatrs_ in liblapack.a(zlatrs.o)
>  "_zdscal_", referenced from:
>      _zgeev_ in liblapack.a(zgeev.o)
>      _zgebak_ in liblapack.a(zgebak.o)
>      _zgebal_ in liblapack.a(zgebal.o)
>      _ztrevc_ in liblapack.a(ztrevc.o)
>      _zlatrs_ in liblapack.a(zlatrs.o)
>      _zlarfg_ in liblapack.a(zlarfg.o)
>  "_zgemm_", referenced from:
>      ___gyre_sysmtx_MOD_factorize_slu_c_._omp_fn.3 in libgyre.a(gyre_sysmtx.o)
>      ___gyre_magnus_ivp_MOD_solve_ in libgyre.a(gyre_magnus_ivp.o)
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgetrf_ in liblapack.a(zgetrf.o)
>      _zgehrd_ in liblapack.a(zgehrd.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlarfb_ in liblapack.a(zlarfb.o)
>      ...
>  "_zgemv_", referenced from:
>      ___gyre_sysmtx_MOD_null_vector_slu_c_._omp_fn.2 in libgyre.a(gyre_sysmtx.o)
>      _zgbtrs_ in liblapack.a(zgbtrs.o)
>      _ztrevc_ in liblapack.a(ztrevc.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlarf_ in liblapack.a(zlarf.o)
>      _zlarft_ in liblapack.a(zlarft.o)
>  "_zgerc_", referenced from:
>      _zlarf_ in liblapack.a(zlarf.o)
>  "_zgeru_", referenced from:
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgbtrs_ in liblapack.a(zgbtrs.o)
>      _zgbtf2_ in liblapack.a(zgbtf2.o)
>      _zgetf2_ in liblapack.a(zgetf2.o)
>  "_zscal_", referenced from:
>      ___gyre_magnus_ivp_MOD_solve_ in libgyre.a(gyre_magnus_ivp.o)
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgbtf2_ in liblapack.a(zgbtf2.o)
>      _zgeev_ in liblapack.a(zgeev.o)
>      _zgetf2_ in liblapack.a(zgetf2.o)
>      _zlahqr_ in liblapack.a(zlahqr.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      ...
>  "_zswap_", referenced from:
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgbtrs_ in liblapack.a(zgbtrs.o)
>      _zgbtf2_ in liblapack.a(zgbtf2.o)
>      _zgetf2_ in liblapack.a(zgetf2.o)
>      _zgebak_ in liblapack.a(zgebak.o)
>      _zgebal_ in liblapack.a(zgebal.o)
>  "_ztbsv_", referenced from:
>      _zgbtrs_ in liblapack.a(zgbtrs.o)
>  "_ztrmm_", referenced from:
>      _zgehrd_ in liblapack.a(zgehrd.o)
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlarfb_ in liblapack.a(zlarfb.o)
>      _zlaqr5_ in liblapack.a(zlaqr5.o)
>  "_ztrmv_", referenced from:
>      _zlahr2_ in liblapack.a(zlahr2.o)
>      _zlarft_ in liblapack.a(zlarft.o)
>  "_ztrsm_", referenced from:
>      ___gyre_sysmtx_MOD_factorize_slu_c_._omp_fn.3 in libgyre.a(gyre_sysmtx.o)
>      ___gyre_sysmtx_MOD_null_vector_slu_c_.constprop.5 in libgyre.a(gyre_sysmtx.o)
>      _zgbtrf_ in liblapack.a(zgbtrf.o)
>      _zgetrf_ in liblapack.a(zgetrf.o)
>      _zgetrs_ in liblapack.a(zgetrs.o)
>  "_ztrsv_", referenced from:
>      _zlatrs_ in liblapack.a(zlatrs.o)
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
> make: *** [tester] Error 1
>
> /Mesa/mesa-r7503/gyre/test
> FAILED
>
>
> /Mesa/mesa-r7503/gyre
> ./build_and_test FAILED
>
> _______________________________________________
>
> I checked my .bashrc just now and it seems to have the same stuff in it as my .bash_profile.
> I assumed having the same stuff in both would not cause a problem?
>
> Thanks,
>
> Chris
>
>
> _________________________________
> From: Josiah Schwab <jwschwab at berkeley.edu>
> Sent: 20 April 2015 18:07
> To: Richard Townsend
> Cc: Manser, Christopher
> Subject: Re: [mesa-users] /Mesa/mesa-r7503/mtx/test FAILED. gfortran.exec error.
>
> Hi Rich,
>
>> Hmm, this is a real puzzle. For some reason, the scripts are working
>> from the command line but not from the build system.
>
> Christopher said that he set the variables in .bash_profile, so I'm
> going to wildly speculate that this is path problem associated with the
> difference between login (.bash_profile) and non-login (.bashrc) shells.
>
> Just a thought,
> Josiah
>
>
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