Errors accessing libhdf5_fortran.so.102 and writing pulsations in MESA prepackaged version of GYRE 5.2

[diogo.capelo]

Hello,

I've recently upgraded to MESA 12115 (and MESASDK 20190830) in Ubuntu 19.04 (in VirtualBox running on Windows 10) and have been trying to get the MESA-prepackaged version of GYRE (5.2, I believe) to work. After compiling the code successfully with 'make', when I try to run the tests by doing 'make test' I get the following output:

Code: Select all

TEST numerics (OpenMP)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (band matrix)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (*_DELTA frequency units)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (rotation, Doppler shift)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (rotation, traditional approximation)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (Cowling approximation)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (DZIEM variables)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (JCD variables)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (MIX variables)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (LAGP variables)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (HDF5 output)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (Collocation difference schemes)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (Magnus difference schemes)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (MIRK difference schemes)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST numerics (Trapezoidal difference scheme)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
TEST polytrope model (n_poly=0.0)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=0.0 w/ double point)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=1.5)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=1.5, no center)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=3.0)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=3.0, g modes)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=3.0 w/ double point)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST polytrope model (n_poly=4.0)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
TEST FGONG solar model S...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
TEST LOSC RGB model...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
TEST MESA model for beta Cephei star (adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for slowly pulsating B-type star (adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for slowly pulsating B-type star (adiabatic, quasi-adiabatic eigfuncs)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for RGB star (adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for delta Cephei star (adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
make[2]: *** [Makefile:11: test] Error 2
TEST MESA model for beta Cephei star (non-adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for slowly pulsating B-type star (non-adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for slowly pulsating B-type star (non-adiabatic, Rossby modes)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for RGB star (non-adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for delta Cephei star (non-adiabatic)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
TEST MESA model for Sun (non-adiabatic, diffusion vs. Eddington approxiation)...
./gyre: error while loading shared libraries: libhdf5_fortran.so.102: cannot open shared object file: No such file or directory
 ...failed: ./gyre returned non-zero exit status
make[4]: *** [Makefile:7: test] Error 1
make[3]: *** [Makefile:11: test] Error 2
make[2]: *** [Makefile:11: test] Error 2
make[1]: *** [Makefile:11: test] Error 2
make: *** [Makefile:15: test] Error 2

The environment variables for MESASDK, GYRE and MESA all look good to me:

Code: Select all

echo $MESA_DIR
/home/diogocapelo/Software/mesa
echo $GYRE_DIR
/home/diogocapelo/Software/mesa/gyre/gyre
echo $MESASDK_ROOT
/home/diogocapelo/Software/mesasdk

From the error output, it seems to me that the problem lies with the file libhdf5_fortran.so.102, which I found to be located at /mesasdk/lib. The links there appear to be working:

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diogocapelo@denebola:~$ ls -l $MESASDK_ROOT/lib | grep libhdf5_fortran.so.102
lrwxrwxrwx 1 diogocapelo diogocapelo        26 ago 30 14:18 libhdf5_fortran.so -> libhdf5_fortran.so.102.0.0
lrwxrwxrwx 1 diogocapelo diogocapelo        26 ago 30 14:18 libhdf5_fortran.so.102 -> libhdf5_fortran.so.102.0.0
-rwxr-xr-x 1 diogocapelo diogocapelo    409596 ago 30 14:20 libhdf5_fortran.so.102.0.0

Looking around the web revealed a few other people with similar problems regarding this file, and a suggested fix was to add a file with the path to the directory where this file is to /etc/ld.so.conf.d, and when I did this, GYRE runs all the tests succesfully. However, a few other applications in my machine stop working entirely (like nano).

I'm also having another issue, which I'm not sure whether it's related or not to the previous one: I've also experienced problems trying to get MESA to write the pulsation files for GYRE. For instance, when I add to my MESA inlist (which runs fine otherwise):

Code: Select all

      write_pulse_data_with_profile = .true.
      pulse_data_format = 'GYRE'
      add_atmosphere_to_pulse_data = .true.

I get the following error the very first time MESA tries to write out a *.GYRE.data file:

Code: Select all

save gs98_calibration/profile1.dataSTOP Invalid cell index in get_gyre_data
free(): corrupted unsorted chunks

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0  0x7ff7efc0c46f in ???
#1  0x7ff7efc0c3eb in ???
#2  0x7ff7efbeb898 in ???
#3  0x7ff7efc5638d in ???
#4  0x7ff7efc5e4db in ???
#5  0x7ff7efc60211 in ???
#6  0x7ff7f070921a in destroy_unit_mutex
	at /root/sdk2/build/gcc/libgfortran/io/unit.c:257
#7  0x7ff7f070921a in close_unit_1
	at /root/sdk2/build/gcc/libgfortran/io/unit.c:759
#8  0x7ff7f05dfd6e in ???
./rn: line 8:  4545 Aborted                 (core dumped) ./star
DATE: 2019-11-11
TIME: 18:16:53

I get this error whether or not I edit /etc/ld.so.conf.d (so, whether or not GYRE actually succesfully runs the tests or not), so I'm guessing it might be something else.

Any insight you can provide into what might be causing these errors is greatly appreciated. Also, please let me know if there's any additional information that may be helpful.

Thanks in advance,
Diogo Capelo

[rhtownsend]

Hi Diogo --

Thanks for your detailed bug report. Let's try to fix the HDF5 issue first. Can you tell me the output from the following commands:

echo $PATH

which gfortran

readelf -d $GYRE_DIR/bin/gyre

cheers,

Rich

[diogo.capelo]

Hello again, and thank you for your reply. Here's what I get when I input the commands you mentioned:

echo $PATH

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/home/diogocapelo/Software/mesasdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

which gfortran

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/home/diogocapelo/Software/mesasdk/bin/gfortran

readelf -d $GYRE_DIR/bin/gyre

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Dynamic section at offset 0x1a1d70 contains 35 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libhdf5_fortran.so.102]
 0x0000000000000001 (NEEDED)             Shared library: [libhdf5.so.103]
 0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [liblapack95.so]
 0x0000000000000001 (NEEDED)             Shared library: [liblapack.so]
 0x0000000000000001 (NEEDED)             Shared library: [libxblas.so]
 0x0000000000000001 (NEEDED)             Shared library: [libblas.so]
 0x0000000000000001 (NEEDED)             Shared library: [libgfortran.so.5]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgomp.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libquadmath.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x000000000000001d (RUNPATH)            Library runpath: [/home/diogocapelo/mesasdk/lib:/home/diogocapelo/mesasdk/lib64]
 0x000000000000000c (INIT)               0x404000
 0x000000000000000d (FINI)               0x557ff4
 0x0000000000000004 (HASH)               0x400320
 0x000000006ffffef5 (GNU_HASH)           0x400820
 0x0000000000000005 (STRTAB)             0x4019f8
 0x0000000000000006 (SYMTAB)             0x400888
 0x000000000000000a (STRSZ)              3714 (bytes)
 0x000000000000000b (SYMENT)             24 (bytes)
 0x0000000000000015 (DEBUG)              0x0
 0x0000000000000003 (PLTGOT)             0x5a3000
 0x0000000000000002 (PLTRELSZ)           4032 (bytes)
 0x0000000000000014 (PLTREL)             RELA
 0x0000000000000017 (JMPREL)             0x402c60
 0x0000000000000007 (RELA)               0x402b10
 0x0000000000000008 (RELASZ)             336 (bytes)
 0x0000000000000009 (RELAENT)            24 (bytes)
 0x000000006ffffffe (VERNEED)            0x4029f0
 0x000000006fffffff (VERNEEDNUM)         6
 0x000000006ffffff0 (VERSYM)             0x40287a
 0x0000000000000000 (NULL)               0x0
 

[rhtownsend]

It looks like you moved the SDK since you compiled GYRE. When you compiled, the SDK was in

/home/diogocapelo/mesasdk

But now it is in

/home/diogocapelo/Software/mesasdk

I suggest you try recompiling GYRE by running 'make clean' and then 'make'.

cheers.

Rich

[diogo.capelo]

Ah, that is absolutely right. Thank you. I did move both MESA and the MESASDK and forgot to recompile them. After following your suggestion, GYRE runs all the tests successfully: sorry about the newbie mistake.

For good measure, I've reinstalled MESA from the new directory (and recompiled and re-tested GYRE with success after doing so), and tested my MESA inlist again. Unfortunately, I'm still get the same error as before (copied here below) when the run tries to write out the first GYRE pulsations.

Code: Select all

save gs98_calibration/profile1.dataSTOP Invalid cell index in get_gyre_data
free(): corrupted unsorted chunks

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0  0x7f66368b946f in ???
#1  0x7f66368b93eb in ???
#2  0x7f6636898898 in ???
#3  0x7f663690338d in ???
#4  0x7f663690b4db in ???
#5  0x7f663690d211 in ???
#6  0x7f66373b621a in destroy_unit_mutex
	at /root/sdk2/build/gcc/libgfortran/io/unit.c:257
#7  0x7f66373b621a in close_unit_1
	at /root/sdk2/build/gcc/libgfortran/io/unit.c:759
#8  0x7f663728cd6e in ???
./rn: line 8: 26454 Aborted                 (core dumped) ./star
DATE: 2019-11-12
TIME: 16:34:00

Any ideas about this one as well, or should I ask this question in the MESA-users mailing list? Thank you again!

[rhtownsend]

I'd suggest you post it to MESA-users, since it is more MESA-related than GYRE-releted.

However, I expect I'll probably be the one that fixes it -- I maintain the code that writes out GYRE models. When you post, be sure to include inlists, version numbers, and anything else that's required to reproduce the problem.

cheers,

Rich