[mesa-users] Can't install MESA (mtx package)

Sat Aug 2 07:50:33 EDT 2014

Hi Nikhil,

Try to ./clean; ./install while being super user.

Cheers!
Shervin

On Sat, Aug 2, 2014 at 10:32 AM, <mesa-users-request at lists.sourceforge.net>
wrote:

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>    1. Re: Install fail on Linux Mint 17 (Pablo Marchant)
>    2. Re: Can't install MESA (mtx package) (Nikhil Mahajan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 1 Aug 2014 15:57:17 +0200
> From: Pablo Marchant <pamarca at gmail.com>
> Subject: Re: [mesa-users] Install fail on Linux Mint 17
> To: Jared Brooks <jcbrooks at physics.ucsb.edu>
> Cc: "mesa-users at lists.sourceforge.net"
>         <mesa-users at lists.sourceforge.net>,     Robert FARMER <
> rjfarmer at asu.edu>
> Message-ID:
>         <CAF_dd5O3agWypf8sYM8p=mS4_Un=
> P7vMj8cVRdSVRaLkNukMfw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Just want to add that I'm using the latest MESA release with the latest SDK
> on mint 17, and I don't have any issues. Don't think it would make any
> difference but I have the SDK on my home folder.
>
> Cheers!
>
>
> On Thu, Jul 31, 2014 at 11:12 PM, Jared Brooks <jcbrooks at physics.ucsb.edu>
> wrote:
>
> > Hey Rich,
> >
> > Here is the output for that (btw, I know the sdk doesn't need to be in
> > /opt anymore, but i put it there just in case):
> >
> > Driving: /opt/mesasdk/bin/gfortran.exec -ffpe-summary=none
> > -I/usr/include/x86_64-linux-gnu -v -o hellow hellow.f90 -l gfortran -l m
> > -shared-libgcc
> > Using built-in specs.
> > COLLECT_GCC=/opt/mesasdk/bin/gfortran.exec
> >
> >
> COLLECT_LTO_WRAPPER=/opt/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.10.0/lto-wrapper
> > Target: x86_64-pc-linux-gnu
> > Configured with: ./configure CC=gcc --build=x86_64-pc-linux-gnu
> > --prefix=/root/mesasdk --with-gmp=/root/mesasdk --with-mpfr=/root/mesasdk
> > --with-mpc=/root/mesasdk --enable-languages=c,c++,fortran
> > --disable-multilib --disable-nls --disable-libsanitizer
> > Thread model: posix
> > gcc version 4.10.0 20140710 (experimental) (GCC)
> > COLLECT_GCC_OPTIONS='-ffpe-summary=none' '-I'
> > '/usr/include/x86_64-linux-gnu' '-v' '-o' 'hellow' '-shared-libgcc'
> > '-mtune=generic' '-march=x86-64'
> >  /opt/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.10.0/f951
> > hellow.f90 -I /usr/include/x86_64-linux-gnu -quiet -dumpbase hellow.f90
> > -mtune=generic -march=x86-64 -auxbase hellow -version -ffpe-summary=none
> > -fintrinsic-modules-path
> > /opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/finclude -o
> > /tmp/ccovoyju.s
> > GNU Fortran (GCC) version 4.10.0 20140710 (experimental)
> > (x86_64-pc-linux-gnu)
> >     compiled by GNU C version 4.10.0 20140710 (experimental), GMP version
> > 5.1.3, MPFR version 3.1.2, MPC version 1.0.2
> > GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
> > GNU Fortran (GCC) version 4.10.0 20140710 (experimental)
> > (x86_64-pc-linux-gnu)
> >     compiled by GNU C version 4.10.0 20140710 (experimental), GMP version
> > 5.1.3, MPFR version 3.1.2, MPC version 1.0.2
> > GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
> > COLLECT_GCC_OPTIONS='-ffpe-summary=none' '-I'
> > '/usr/include/x86_64-linux-gnu' '-v' '-o' 'hellow' '-shared-libgcc'
> > '-mtune=generic' '-march=x86-64'
> >  as -v -I /usr/include/x86_64-linux-gnu --64 -o /tmp/ccWYrvfN.o
> > /tmp/ccovoyju.s
> > GNU assembler version 2.24 (x86_64-linux-gnu) using BFD version (GNU
> > Binutils for Ubuntu) 2.24
> > Reading specs from
> >
> /opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/../../../../lib64/libgfortran.spec
> > rename spec lib to liborig
> > COLLECT_GCC_OPTIONS='-ffpe-summary=none' '-I'
> > '/usr/include/x86_64-linux-gnu' '-v' '-o' 'hellow' '-shared-libgcc'
> > '-mtune=generic' '-march=x86-64'
> >
> >
> COMPILER_PATH=/opt/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.10.0/:/opt/mesasdk/bin/../libexec/gcc/
> >
> >
> LIBRARY_PATH=/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/:/opt/mesasdk/bin/../lib/gcc/:/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/x86_64-linux-gnu/:./:/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/../../../:/lib/:/usr/lib/
> > COLLECT_GCC_OPTIONS='-ffpe-summary=none' '-I'
> > '/usr/include/x86_64-linux-gnu' '-v' '-o' 'hellow' '-shared-libgcc'
> > '-mtune=generic' '-march=x86-64'
> >  /opt/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.10.0/collect2
> > --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2
> -o
> > hellow crt1.o crti.o
> > /opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/crtbegin.o
> > -L/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0
> > -L/opt/mesasdk/bin/../lib/gcc
> >
> -L/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/../../../../lib64
> > -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L.
> > -L/opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/../../..
> > /tmp/ccWYrvfN.o -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc
> > -lc -lgcc_s -lgcc
> > /opt/mesasdk/bin/../lib/gcc/x86_64-pc-linux-gnu/4.10.0/crtend.o crtn.o
> >
> > /usr/bin/ld: cannot find crt1.o: No such file or directory
> > /usr/bin/ld: cannot find crti.o: No such file or directory
> > /usr/bin/ld: cannot find -lm
> > /usr/bin/ld: cannot find -lm
> > /usr/bin/ld: cannot find -lc
> > /usr/bin/ld: cannot find crtn.o: No such file or directory
> > collect2: error: ld returned 1 exit status
> >
> >
> >
> > Rob, those export commands didn't change anything.
> >
> > -Jared
> >
> >
> > On Thu, Jul 31, 2014 at 2:02 PM, Richard Townsend <
> townsend at astro.wisc.edu
> > > wrote:
> >
> >> Hi Jared ?
> >>
> >> Try this: cut and paste the program below into hellow.f90, and then do
> >>
> >> gfortran -v -o hellow hellow.f90
> >>
> >> Can you send the output printed during compilation?
> >>
> >> cheers,
> >>
> >> Rich
> >>
> >> ?CUT?
> >> program hellow
> >>   print *,'hello world'
> >> end program hellow
> >> ?CUT?
> >>
> >> On Jul 31, 2014, at 3:50 PM, Jared Brooks <jcbrooks at physics.ucsb.edu>
> >> wrote:
> >>
> >> Hi Rob,
> >>
> >> Both those folders exist on my system.
> >>
> >> I have tried a few fresh checkouts, I tried some of the things suggested
> >> in the thread a couple weeks ago, such as:
> >> export LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
> >> export C_INCLUDE_PATH=/usr/include/x86_64-linux-gnu/
> >>
> >> These seemed to change results for the person who first tried these, but
> >> I got the exact same error message every time.
> >>
> >> Here is the output for "gfortran --version"
> >> GNU Fortran (GCC) 4.10.0 20140710 (experimental)
> >>
> >> -Jared
> >>
> >>
> >> On Thu, Jul 31, 2014 at 1:33 PM, Robert FARMER <rjfarmer at asu.edu>
> wrote:
> >>
> >>> Hmm, mints a derivative of ubunut/debain so the new wrapper script
> >>> should of taken care of it.
> >>>
> >>> Do any of the following folders exist on your system?
> >>>  /usr/lib64
> >>> /usr/lib/x86_64-linux-gnu
> >>>
> >>> And which steps specifically have you tried? and have you also tried a
> >>> clean checkout? I know you said gfortran --version gives the correct
> >>> output, but what is that just in case your terminal has the old sdk
> loaded
> >>> by accident.
> >>>
> >>> Rob
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, Jul 31, 2014 at 12:02 PM, Jared Brooks <
> >>> jcbrooks at physics.ucsb.edu> wrote:
> >>>
> >>>> Hello mesa-users,
> >>>>
> >>>> I am trying to install version 6596 on Linux Mint 17. I installed the
> >>>> most recent sdk, "gfortran --version" gives the correct output. I
> looked
> >>>> through the archives for similar problems and tried some of their
> >>>> solutions, but I get the same error every time:
> >>>>
> >>>> /home/jcbrooks/mesa_6596/const
> >>>> building const package.
> >>>>
> >>>> make: `libconst.a' is up to date.
> >>>> make: `libconst.a' is up to date.
> >>>> gfortran -fopenmp -o ../tester test_const.o -L../../make -lconst
> >>>>
> >>>> /usr/bin/ld: cannot find crt1.o: No such file or directory
> >>>> /usr/bin/ld: cannot find crti.o: No such file or directory
> >>>> /usr/bin/ld: cannot find -lm
> >>>> /usr/bin/ld: cannot find -lm
> >>>> /usr/bin/ld: cannot find -lpthread
> >>>> /usr/bin/ld: cannot find -lc
> >>>> /usr/bin/ld: cannot find crtn.o: No such file or directory
> >>>>
> >>>> collect2: error: ld returned 1 exit status
> >>>> make: *** [tester] Error 1
> >>>>
> >>>> /home/jcbrooks/mesa_6596/
> >>>> const/test
> >>>> FAILED
> >>>>
> >>>>
> >>>> /home/jcbrooks/mesa_6596/const
> >>>> ./build_and_test FAILED
> >>>>
> >>>>
> >>>>
> >>>> I don't have too much experience with Linux, so any help would be
> >>>> greatly appreciated, thanks.
> >>>>
> >>>> -Jared
> >>>>
> >>>>
> >>>>
> ------------------------------------------------------------------------------
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> >>>>
> >>>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
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> >>> Build a bridge from your legacy apps to the future.
> >>>
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> >>> https://lists.sourceforge.net/lists/listinfo/mesa-users
> >>>
> >>>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Infragistics Professional
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> >> Build a bridge from your legacy apps to the future.
> >>
> >>
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> >> https://lists.sourceforge.net/lists/listinfo/mesa-users
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Infragistics Professional
> >> Build stunning WinForms apps today!
> >> Reboot your WinForms applications with our WinForms controls.
> >> Build a bridge from your legacy apps to the future.
> >>
> >>
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> >>
> >>
> >
> >
> >
> ------------------------------------------------------------------------------
> > Infragistics Professional
> > Build stunning WinForms apps today!
> > Reboot your WinForms applications with our WinForms controls.
> > Build a bridge from your legacy apps to the future.
> >
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
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> >
> >
>
>
> --
> Pablo Marchant Campos
> M.Sc on Astrophysics, Universidad Cat?lica de Chile
> PhD student, Argelander-Institut f?r Astronomie
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> ------------------------------
>
> Message: 2
> Date: Sat, 2 Aug 2014 03:55:36 -0400
> From: Nikhil Mahajan <nikhil.mahajan at utoronto.ca>
> Subject: Re: [mesa-users] Can't install MESA (mtx package)
> To: mesa-users at lists.sourceforge.net
> Message-ID:
>         <
> CAA39X0JjMUCki1Ez21bUZH808CT+2dwh5dLK20nXijO6k7m0Zg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> I am trying to install *MESA (release 6208)* using *MESASDK (version
> 20140313)*, and get the following error during installation:
>
> make: Nothing to be done for `all'.
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero
> -fopenmp -I../../make -I../../public -I../../../include
> -I/mnt/raid-cita/mahajann/MESA6208/mesasdk/include -fbounds-check
> -Wuninitialized -Warray-bounds -g -c -ffree-form -x f95-cpp-input
> ../src/test_mtx_support.f
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero
> -fopenmp -I../../make -I../../public -I../../../include
> -I/mnt/raid-cita/mahajann/MESA6208/mesasdk/include -fbounds-check
> -Wuninitialized -Warray-bounds -g -c -ffree-form -x f95-cpp-input -x
> f95-cpp-input -DDBLE -o test_block_tri_dble.o
> ../src/test_block_tridiagonal.f
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero
> -fopenmp -I../../make -I../../public -I../../../include
> -I/mnt/raid-cita/mahajann/MESA6208/mesasdk/include -fbounds-check
> -Wuninitialized -Warray-bounds -g -c -ffree-form -x f95-cpp-input -x
> f95-cpp-input -DDBLE -o test_klu_dble.o ../src/test_klu.f
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero
> -fopenmp -I../../make -I../../public -I../../../include
> -I/mnt/raid-cita/mahajann/MESA6208/mesasdk/include -fbounds-check
> -Wuninitialized -Warray-bounds -g -c -ffree-form -x f95-cpp-input
> ../src/test_sparse.f
> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens -fno-sign-zero
> -fopenmp -I../../make -I../../public -I../../../include
> -I/mnt/raid-cita/mahajann/MESA6208/mesasdk/include -fbounds-check
> -Wuninitialized -Warray-bounds -g -c -ffree-form -x f95-cpp-input
> ../src/test_mtx.f
> gfortran -fopenmp -o ../tester test_mtx_support.o test_block_tri_dble.o
> test_klu_dble.o test_sparse.o test_mtx.o  -L../../make -lf2crlibm -lcrlibm
> -lmtx -lconst -lutils -lmesaklu `mesasdk_lapack_link` `mesasdk_blas_link`
> -L../../../lib
> ../../make/libmtx.a(mtx_support.o): In function
> `__mtx_support_MOD_do_quad_block_multiply_xa':
> mtx_support.f:(.text+0x2319): undefined reference to `GOMP_parallel'
> ../../make/libmtx.a(mtx_support.o): In function
> `__mtx_support_MOD_do_block_multiply_xa':
> mtx_support.f:(.text+0x2379): undefined reference to `GOMP_parallel'
> ../../make/libmtx.a(mtx_support.o): In function
> `__mtx_support_MOD_do_lu_factored_block_dble_mv':
> mtx_support.f:(.text+0x415f): undefined reference to `GOMP_parallel'
> ../../make/libmtx.a(mtx_support.o): In function
> `__mtx_support_MOD_do_block_mv_quad':
> mtx_support.f:(.text+0x41f5): undefined reference to `GOMP_parallel'
> ../../make/libmtx.a(mtx_support.o): In function
> `__mtx_support_MOD_do_band_to_row_sparse':
> mtx_support.f:(.text+0x756a): undefined reference to `GOMP_parallel'
> ../../make/libmtx.a(bcyclic.o):bcyclic.f:(.text+0x2cde): more undefined
> references to `GOMP_parallel' follow
> collect2: error: ld returned 1 exit status
> make: *** [tester] Error 1
>
> /mnt/raid-cita/mahajann/MESA6208/mesa/mtx/test
> FAILED
>
>
> /mnt/raid-cita/mahajann/MESA6208/mesa/mtx
> ./build_and_test FAILED
>
> ----
> Here's some extra information:
>
> *[mahajann at tpb4 mesa]$ uname -a*
> Linux tpb4 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC 2012
> x86_64 x86_64 x86_64 GNU/Linux
> *[mahajann at tpb4 mesa]$ gfortran -v*
> Using built-in specs.
> COLLECT_GCC=/mnt/raid-cita/mahajann/MESA6208/mesasdk/bin/gfortran.exec
>
> COLLECT_LTO_WRAPPER=/mnt/raid-cita/mahajann/MESA6208/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/4.9.0/lto-wrapper
> Target: x86_64-pc-linux-gnu
> Configured with: ./configure CC=gcc --build=x86_64-pc-linux-gnu
> --prefix=/root/mesasdk --with-gmp=/root/mesasdk --with-mpfr=/root/mesasdk
> --with-mpc=/root/mesasdk --enable-languages=c,c++,fortran
> --disable-multilib --disable-nls --disable-libsanitizer
> Thread model: posix
> gcc version 4.9.0 20140201 (experimental) (GCC)
> *[mahajann at tpb4 mesa]$ echo $MESASDK_ROOT*
> /mnt/raid-cita/mahajann/MESA6208/mesasdk
> *[mahajann at tpb4 mesa]$ echo $PATH*
>
> /mnt/raid-cita/mahajann/MESA6208/mesasdk/bin:/opt/python/2.7.6/bin:/opt/gcc/4.8.2/bin/:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/opt/c3-4/:/opt/maui-3.3.1/bin:/opt/torque-2.5.12/bin:/opt/torque-2.5.12/sbin:/opt/pegasus/3.1/bin:/opt/dell/srvadmin/bin:/opt/openmpi/1.6.5-gcc-4.8.2/bin
>
> ----
>
> What can I do to fix this issue? Please advise.
>
> Thanks!
>
> Regards,
> Nikhil Mahajan
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