[Mesa-users] MESA Installation Error

Tsantiri, Artemis tsantiri at frib.msu.edu
Mon Jun 27 20:08:12 UTC 2022 

I'm sorry I missed the first output:

[tsantiri at dev-amd20-v100 test]$ free
              total        used        free      shared  buff/cache   available
Mem:      196459380   114281980    65821336     1484316    16356064    79942108
Swap:             0           0           0



Artemis Tsantiri
Graduate Assistant
Facility for Rare Isotope Beams
Michigan State University
640 South Shaw Lane
East Lansing, MI 48824, USA
Email: tsantiri at frib.msu.edu<mailto:tsantiri at frib.msu.edu>
________________________________
From: Tsantiri, Artemis
Sent: Monday, June 27, 2022 4:07:14 PM
To: RICHARD H D TOWNSEND
Cc: Rob Farmer; mesa-users
Subject: Re: [Mesa-users] MESA Installation Error


Hello,


[tsantiri at dev-amd20-v100 test]$ ldd $MESA_DIR/const/test/tester
    linux-vdso.so.1 =>  (0x00007ffe18bc6000)
    libgfortran.so.3 => /opt/software/GCCcore/6.4.0/lib64/libgfortran.so.3 (0x00002b12b3fa8000)
    libm.so.6 => /lib64/libm.so.6 (0x00002b12b42ce000)
    libgomp.so.1 => /mnt/home/tsantiri/mesasdk/lib64/libgomp.so.1 (0x00002b12b45d0000)
    libgcc_s.so.1 => /mnt/home/tsantiri/mesasdk/lib64/libgcc_s.so.1 (0x00002b12b4811000)
    libquadmath.so.0 => /mnt/home/tsantiri/mesasdk/lib64/libquadmath.so.0 (0x00002b12b4a29000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b12b4c70000)
    libc.so.6 => /lib64/libc.so.6 (0x00002b12b4e8c000)
    /lib64/ld-linux-x86-64.so.2 (0x00002b12b3d84000)
    librt.so.1 => /lib64/librt.so.1 (0x00002b12b525a000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00002b12b5462000)

Thanks,



Artemis Tsantiri
Graduate Assistant
Facility for Rare Isotope Beams
Michigan State University
640 South Shaw Lane
East Lansing, MI 48824, USA
Email: tsantiri at frib.msu.edu<mailto:tsantiri at frib.msu.edu>
________________________________
From: RICHARD H D TOWNSEND <townsend at astro.wisc.edu>
Sent: Monday, June 27, 2022 4:03:30 PM
To: Tsantiri, Artemis
Cc: Rob Farmer; mesa-users
Subject: Re: [Mesa-users] MESA Installation Error

[EXTERNAL] This email originated from outside of FRIB

Thanks, Artemis. Here are couple more useful commands to run and post output:

free
ldd $MESA_DIR/const/test/tester

cheers,

Rich

On Jun 27, 2022, at 3:00 PM, Tsantiri, Artemis via Mesa-users <mesa-users at lists.mesastar.org<mailto:mesa-users at lists.mesastar.org>> wrote:

Hi Rob,

Here's the output:

[tsantiri at dev-amd20-v100 test]$ /usr/bin/gdb ./tester -ex r -ex bt
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-120.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /mnt/ufs18/home-205/tsantiri/mesa-r21.12.1/const/test/tester...done.
Starting program: /mnt/ufs18/home-205/tsantiri/mesa-r21.12.1/const/test/./tester
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".

Program received signal SIGSEGV, Segmentation fault.
format_hash (dtp=0x7fffffff62d0, dtp=0x7fffffff62d0) at ../../../libgfortran/io/format.c:129
129    ../../../libgfortran/io/format.c: No such file or directory.
#0  format_hash (dtp=0x7fffffff62d0, dtp=0x7fffffff62d0) at ../../../libgfortran/io/format.c:129
#1  find_parsed_format (dtp=0x7fffffff62d0) at ../../../libgfortran/io/format.c:164
#2  _gfortrani_parse_format (dtp=dtp at entry=0x7fffffff62d0) at ../../../libgfortran/io/format.c:1229
#3  0x00002aaaaadb1828 in data_transfer_init (dtp=0x7fffffff62d0, read_flag=0) at ../../../libgfortran/io/transfer.c:2481
#4  0x0000000000400b75 in do_test_const () at ../src/test_const.f:27
#5  0x000000000040191c in test_const () at ../src/test_const.f:16
#6  0x0000000000401952 in main (argc=1, argv=0x7fffffff703c) at ../src/test_const.f:2
#7  0x00002aaaabbd5555 in __libc_start_main () from /lib64/libc.so.6
#8  0x0000000000400a19 in _start ()
Missing separate debuginfos, use: debuginfo-install glibc-2.17-325.el7_9.x86_64
(gdb)
Is this "debuginfo-install glibc-2.17-325.el7_9.x86_64" a command I should try? Please note that I do not have sudo privileges in this server, but I can contact IT if a package needs to be installed.

Also:
[tsantiri at dev-amd20-v100 test]$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 1
file size               (blocks, -f) unlimited
pending signals                 (-i) 767324
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 51200
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) 7200
max user processes              (-u) 4096
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Thanks,
Artemis




Artemis Tsantiri
Graduate Assistant
Facility for Rare Isotope Beams
Michigan State University
640 South Shaw Lane
East Lansing, MI 48824, USA
Email: tsantiri at frib.msu.edu<mailto:tsantiri at frib.msu.edu>
________________________________
From: Rob Farmer <robert.j.farmer37 at gmail.com<mailto:robert.j.farmer37 at gmail.com>>
Sent: Monday, June 27, 2022 3:47:07 PM
To: Tsantiri, Artemis
Cc: mesa-users
Subject: Re: [Mesa-users] MESA Installation Error

[EXTERNAL] This email originated from outside of FRIB

Hi,

Can you try:
cd $MESA_DIR/const/test
/usr/bin/gdb ./tester -ex r -ex bt

and copy the output. To exit gdb type quit then y if prompted

Also what's the output of:
ulimit -a

Thanks
Rob


On Mon, 27 Jun 2022 at 21:27, Tsantiri, Artemis via Mesa-users <mesa-users at lists.mesastar.org<mailto:mesa-users at lists.mesastar.org>> wrote:
Hello Francis,

Here is the content of the build.log:

*** Copy and paste the following information into your email to mesa-users ***

MESA Version
r21.12.1

uname -a
Linux dev-amd20-v100 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

gfortran -v
Using built-in specs.
COLLECT_GCC=/mnt/home/tsantiri/mesasdk/bin/gfortran.exec
COLLECT_LTO_WRAPPER=/mnt/ufs18/home-205/tsantiri/mesasdk/bin/../libexec/gcc/x86_64-pc-linux-gnu/10.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /home/user/sdk2-tmp/build/gcc/configure CC= CXX= --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --target=x86_64-pc-linux-gnu --prefix=/home/user/sdk2-tmp/mesasdk --with-gmp=/home/user/sdk2-tmp/mesasdk --with-mpfr=/home/user/sdk2-tmp/mesasdk --with-mpc=/home/user/sdk2-tmp/mesasdk --enable-languages=c,c++,fortran --disable-multilib --disable-nls --disable-libsanitizer --enable-clocale=generic
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 10.2.0 (GCC)

$MESASDK_ROOT
/mnt/home/tsantiri/mesasdk

MESASDK version
x86_64-linux-21.4.1

$PATH
/mnt/home/tsantiri/mesasdk/bin:/mnt/home/tsantiri/mesasdk/bin:/mnt/home/tsantiri/mesasdk/bin:/opt/software/powertools/bin:/opt/software/MATLAB/2018a:/opt/software/MATLAB/2018a/bin:/opt/software/Java/1.8.0_152:/opt/software/Java/1.8.0_152/bin:/opt/software/Python/3.6.4-foss-2018a/bin:/opt/software/SQLite/3.21.0-GCCcore-6.4.0/bin:/opt/software/Tcl/8.6.8-GCCcore-6.4.0/bin:/opt/software/libreadline/7.0-GCCcore-6.4.0/bin:/opt/software/ncurses/6.0-GCCcore-6.4.0/bin:/opt/software/CMake/3.11.1-GCCcore-6.4.0/bin:/opt/software/bzip2/1.0.6-GCCcore-6.4.0/bin:/opt/software/FFTW/3.3.7-gompi-2018a/bin:/opt/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/bin:/opt/software/imkl/2018.1.163-gompi-2018a/mkl/bin:/opt/software/imkl/2018.1.163-gompi-2018a/bin:/opt/software/OpenMPI/2.1.2-GCC-6.4.0-2.28/bin:/opt/software/binutils/2.28-GCCcore-6.4.0/bin:/opt/software/GCCcore/6.4.0/bin:/usr/lib64/qt-3.3/bin:/opt/software/core/lua/lua/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/hpcc/bin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin

$MESA_DIR
/mnt/home/tsantiri/mesa-r21.12.1


/mnt/home/tsantiri/mesa-r21.12.1/const
building const package.

make: `../tester' is up to date.


FAILED


/mnt/home/tsantiri/mesa-r21.12.1/const/test
TEST FAILED -- compare test_output to tmp.txt


/mnt/home/tsantiri/mesa-r21.12.1/const
./build_and_test FAILED


Thanks,



Artemis Tsantiri
Graduate Assistant
Facility for Rare Isotope Beams
Michigan State University
640 South Shaw Lane
East Lansing, MI 48824, USA
Email: tsantiri at frib.msu.edu<mailto:tsantiri at frib.msu.edu>
________________________________
From: Francis Timmes <fxt44 at mac.com<mailto:fxt44 at mac.com>>
Sent: Monday, June 27, 2022 3:17:01 PM
To: Tsantiri, Artemis
Cc: Frank Timmes; mesa-users
Subject: Re: [Mesa-users] MESA Installation Error

[EXTERNAL] This email originated from outside of FRIB


hi artemis,



there is not enough information provided to offer a diagnosis.

a plain text file named build.log should have been produced that is more informative.

attach this file.



fxt









> On Jun 27, 2022, at 11:49 AM, Tsantiri, Artemis via Mesa-users <mesa-users at lists.mesastar.org<mailto:mesa-users at lists.mesastar.org>> wrote:

>

> Hello,

>

> I'm trying to install MESA version r21.12 on a linux server (CentOS Linux release 7.9.2009) using the SDK package version 21.4.1. I have performed the same installation on my local machine (Ubuntu 20.04) during the last MESA summer school and I didn't encounter any issues, so I do not know what I did wrong this time. I made sure the server has all the prerequisites installed using the rpm -qa | grep {package name} command and I have fortran gcc version 10.2 as in my local machine. The environment variables $MESA_DIR and $MESASDK_ROOT are set correctly and I checked them with the echo command.

>

> This is what I get as I try to install (I tried ./clean and then again ./install and it is reproducible):

>

> [tsantiri at dev-amd20-v100 mesa-r21.12.1]$ ./install

>

> /mnt/home/tsantiri/mesa-r21.12.1/const

> building const package.

>

> MAKEDEPF90

> COMPILE_CMD ../public/const_def.f90

> COMPILE_CMD ../public/const_lib.f90

> LIB_TOOL libconst.a

> MAKEDEPF90

> TEST_COMPILE ../src/test_const.f

> LOADER ../tester

>

>

> FAILED

>

>

> /mnt/home/tsantiri/mesa-r21.12.1/const/test

> TEST FAILED -- compare test_output to tmp.txt

>

>

> /mnt/home/tsantiri/mesa-r21.12.1/const

> ./build_and_test FAILED

>

> The tmp.txt file that it tells me to compare with the test_output file has the following one line:

>

> ./rn: line 3: 27408 Segmentation fault      ./tester

>

> How could I fix this?

> Thank you in advance.

>

> Best,

>

>

> Artemis Tsantiri

> Graduate Assistant

> Facility for Rare Isotope Beams

> Michigan State University

> 640 South Shaw Lane

> East Lansing, MI 48824, USA

> Email: tsantiri at frib.msu.edu<mailto:tsantiri at frib.msu.edu>

> _______________________________________________

> mesa-users at lists.mesastar.org<mailto:mesa-users at lists.mesastar.org>

> https://lists.mesastar.org/mailman/listinfo/mesa-users



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https://lists.mesastar.org/mailman/listinfo/mesa-users

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