Error messages when installing gyre

[beauabrooks]

I got a stream of error messages when MESA attempted to install gyre during my initial install. When I went to to the gyre directory and use make, as in the gyre installation instructions, build_poly was missing from my bin. I am using MadSDK and running on Ubuntu. The error messages I received look like this:

...
gyre/data/tar/tar_fit.m-5.k-1.h5
gyre/data/tar/tar_fit.m-5.k-2.h5
gyre/data/tar/tar_fit.m-5.k-3.h5
gyre/data/tar/tar_fit.m-5.k-4.h5
gyre/data/tar/tar_fit.m-5.k-5.h5
gyre/bin/.empty
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
...

I've tried reinstalling and as far as I know madsdk was installed correctly. I'm not sure how to proceed.

Thanks for the help!

[rhtownsend]

I got a stream of error messages when MESA attempted to install gyre during my initial install. When I went to to the gyre directory and use make, as in the gyre installation instructions, build_poly was missing from my bin. I am using MadSDK and running on Ubuntu. The error messages I received look like this:

...
gyre/data/tar/tar_fit.m-5.k-1.h5
gyre/data/tar/tar_fit.m-5.k-2.h5
gyre/data/tar/tar_fit.m-5.k-3.h5
gyre/data/tar/tar_fit.m-5.k-4.h5
gyre/data/tar/tar_fit.m-5.k-5.h5
gyre/bin/.empty
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
...

I've tried reinstalling and as far as I know madsdk was installed correctly. I'm not sure how to proceed.

Thanks for the help!

Can you post the output of the command 'madsdk_odepack_link'.

cheers,

Rich

[beauabrooks]

I got a stream of error messages when MESA attempted to install gyre during my initial install. When I went to to the gyre directory and use make, as in the gyre installation instructions, build_poly was missing from my bin. I am using MadSDK and running on Ubuntu. The error messages I received look like this:

...
gyre/data/tar/tar_fit.m-5.k-1.h5
gyre/data/tar/tar_fit.m-5.k-2.h5
gyre/data/tar/tar_fit.m-5.k-3.h5
gyre/data/tar/tar_fit.m-5.k-4.h5
gyre/data/tar/tar_fit.m-5.k-5.h5
gyre/bin/.empty
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
...

I've tried reinstalling and as far as I know madsdk was installed correctly. I'm not sure how to proceed.

Thanks for the help!

Can you post the output of the command 'madsdk_odepack_link'.

cheers,

Rich

Here it is:

/home/beauabrooks/madsdk/lib/libodepack.a /home/beauabrooks/madsdk/lib/libblas.a

[rhtownsend]

Here it is:

/home/beauabrooks/madsdk/lib/libodepack.a /home/beauabrooks/madsdk/lib/libblas.a

Hmm, that looks OK. What happens when you run these commands:

cd $GYRE_DIR/src/build
make clean
make build_poly

cheers,

Rich

[beauabrooks]

This is the output when I tried make clean:

beauabrooks@beauabrooks-Q325UA:~/mesa-r10108/gyre/gyre/src/build$ make clean
/bin/sh: 1: Syntax error: Bad fd number
/bin/sh: 1: Syntax error: Bad fd number
rm -f gyre poly_to_fgong gyre.f90 poly_to_fgong.f90 *.o *.mod .depend *.f90

Running make build_poly spits out more of the errors I had before:

/bin/sh: 1: Syntax error: Bad fd number
/bin/sh: 1: Syntax error: Bad fd number
Determining dependencies
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE \s*([a-zA-Z_]\w*)\s*}/ at /home/beauabrooks/madsdk/bin/fpx3 line 233.
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /home/beauabrooks/madsdk/bin/fpx3 line 261.
...

with this tacked at the end:

FC build_poly.f90
build_poly.f90:54:6:

use core_kinds
1
Fatal Error: Can't open module file 'core_kinds.mod' for reading at (1): No such file or directory
compilation terminated.
Make.inc:93: recipe for target 'build_poly.o' failed
make: *** [build_poly.o] Error 1

[rhtownsend]

Those bad fd number errors are very strange. Can you post the output from 'ls -l /bin/sh'

Also, please post output from the following commands:

uname -a
mesasdk_version.sh
gfortran -v

cheers,

Rich

[beauabrooks]

Here it is:

beauabrooks@beauabrooks-Q325UA:~$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Mar 16 19:46 /bin/sh -> dash
beauabrooks@beauabrooks-Q325UA:~$ uname -a
Linux beauabrooks-Q325UA 4.13.0-37-generic #42~16.04.1-Ubuntu SMP Wed Mar 7 16:03:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
beauabrooks@beauabrooks-Q325UA:~$ mesasdk_version.sh
x86_64-linux-20160129
beauabrooks@beauabrooks-Q325UA:~$ gfortran -v
Using built-in specs.
COLLECT_GCC=/home/beauabrooks/madsdk/bin/gfortran.exec
COLLECT_LTO_WRAPPER=/home/beauabrooks/madsdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/5.3.1/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /root/madsdk-src/gcc/configure CC=gcc --build=x86_64-pc-linux-gnu --prefix=/root/madsdk --with-gmp=/root/madsdk --with-mpfr=/root/madsdk --with-mpc=/root/madsdk --enable-languages=c,c++,fortran --disable-multilib --disable-nls --disable-libsanitizer --enable-clocale=generic
Thread model: posix
gcc version 5.3.1 20160129 (GCC)

[rhtownsend]

Here it is:

beauabrooks@beauabrooks-Q325UA:~$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Mar 16 19:46 /bin/sh -> dash
beauabrooks@beauabrooks-Q325UA:~$ uname -a
Linux beauabrooks-Q325UA 4.13.0-37-generic #42~16.04.1-Ubuntu SMP Wed Mar 7 16:03:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
beauabrooks@beauabrooks-Q325UA:~$ mesasdk_version.sh
x86_64-linux-20160129
beauabrooks@beauabrooks-Q325UA:~$ gfortran -v
Using built-in specs.
COLLECT_GCC=/home/beauabrooks/madsdk/bin/gfortran.exec
COLLECT_LTO_WRAPPER=/home/beauabrooks/madsdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/5.3.1/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /root/madsdk-src/gcc/configure CC=gcc --build=x86_64-pc-linux-gnu --prefix=/root/madsdk --with-gmp=/root/madsdk --with-mpfr=/root/madsdk --with-mpc=/root/madsdk --enable-languages=c,c++,fortran --disable-multilib --disable-nls --disable-libsanitizer --enable-clocale=generic
Thread model: posix
gcc version 5.3.1 20160129 (GCC)

Thanks. I think that the fact that the default shell (/bin/sh) is the dash shell may be causing the problems. Can you try adding the following line:

SHELL:=/bin/bash

...to the top of $GYRE_DIR/src/build/Makefile. Then, try doing 'make clean' and 'make' again.

cheers,

Rich

[beauabrooks]

That seemed to have done it, however I had to add the same bit of code to the top of $MESA_DIR/gyre/make/makefile.

[rhtownsend]

That seemed to have done it, however I had to add the same bit of code to the top of $MESA_DIR/gyre/make/makefile.

Excellent -- thanks for the feedback. I'll put these fixes into the next release of GYRE.