Unable to install EGSnrc in Linux

[Abdullah-Abuhaimed]

Dear all,

I am trying to install the last version of EGSnrc in Linux, but I could not find out what the issue is. It seems that there is an issue in the C and g++ compilers, they cannot be identified during the configuration, although there are installed. I have used different versions of GCC including the most recent one (10.2), but none of them worked. Please see the installation process is given below. It would be greatly appreciated if anyone could suggest a solution to overcome the issue.

-bash-4.2$ module load gcc-10.2.0-gcc-4.8.5-3mz7fbw

-bash-4.2$ module show gcc-10.2.0-gcc-4.8.5-3mz7fbw
/mnt/apps/spack/share/spack/modules/linux-centos7-sandybridge/gcc-10.2.0-gcc-4.8.5-3mz7fbw:
module-whatis    The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.
prepend-path     LD_LIBRARY_PATH /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/lib
prepend-path     LD_LIBRARY_PATH /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/lib64
prepend-path     PATH /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin
prepend-path     MANPATH /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/share/man
prepend-path     CMAKE_PREFIX_PATH /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/
setenv           CC /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gcc
setenv           CXX /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/g++
setenv           FC /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran
setenv           F77 /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran

-bash-4.2$ gfortran --version
GNU Fortran (Spack GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

-bash-4.2$ gcc --version
gcc (Spack GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

-bash-4.2$ g++ --version
g++ (Spack GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

-bash-4.2$ make --version
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010  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.

-bash-4.2$ which gfortran
/mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran

-bash-4.2$ which gcc
/mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gcc

-bash-4.2$ which g++
/mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/g++

-bash-4.2$ git --version
git version 2.29.0

-bash-4.2$ git clone https://github.com/nrc-cnrc/EGSnrc.git
Cloning into 'EGSnrc'...
remote: Enumerating objects: 13686, done.
remote: Counting objects: 100% (21/21), done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 13686 (delta 7), reused 12 (delta 5), pack-reused 13665
Receiving objects: 100% (13686/13686), 54.13 MiB | 13.90 MiB/s, done.
Resolving deltas: 100% (9134/9134), done.
Updating files: 100% (2448/2448), done.

-bash-4.2$ export HEN_HOUSE="" EGS_HOME="" EGS_CONFIG=""
-bash-4.2$ cd EGSnrc

-bash-4.2$ ./HEN_HOUSE/scripts/configure

###############################################################################
configure
###############################################################################

Copyright (C) 2015 National Research Council Canada

This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. See LICENCE file for
details or http://www.gnu.org/licenses/agpl.txt

###############################################################################

EGSnrc configuration script.

This script configures EGSnrc for use on your system.  The configuration
options will be saved in a configuration file inside the $HEN_HOUSE/specs
directory. You can use this configuration by setting the environment variable
$EGS_CONFIG to the path of the configuration file.

You can use this script to generate as many different configurations as you
wish (for instance, you may have different compilers installed or various
operating systems on the same file system). If the environment variable
$HEN_HOUSE is set for previous EGSnrc installations, it should probably be
unset prior to calling this script.

This script will ask you questions to configure EGSnrc.

Any response you enter overrides the suggested default shown in brackets.
This implies that if you want to *add* something to the default answer, you
must re-type this default answer as part of your response.

To accept the default answer shown in brackets:     just press enter.
To submit an empty answer, overriding the default:  enter '--' as a response.
To get help for some questions requiring input:     enter '?' as a response.

###############################################################################

You can exit this script at any time by typing Ctrl-C.

Press enter to continue.

Checking system type ...                          x86_64-unknown-linux-gnu
Checking for make ...                             yes (/usr/bin/gmake)

Looking for available fortran compilers ...       found: gfortran f95

Input fortran compiler:                           [gfortran] /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran
Testing if /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran works ... yes. Object extension is 'o'
Testing if /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran can create executables ... yes. Extension is ''
Checking for compiler version ...                 GNU Fortran (Spack GCC) version 10.2.0

Input standard compilation flags:                 [-fPIC]
Input optimization flags:                         [-O2 -mtune=native]
Input flags for debugging:                        [-g]
Input libraries that your compiler may need:

Will use the following compiler settings:
    F77     = /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gfortran
    FCFLAGS = -fPIC
    FDEBUG  = -g
    FOPT    = -O2 -mtune=native
    FLIBS   =

Testing if compilation flags work ...             yes

Checking for the availability of various system dependent functions:
Checking for a working 'exit' subroutine ...      yes (exit)
Checking if 'system' is a function ...            yes
Checking for the 'date_and_time' subroutine ...   yes
Checking for the 'flush' subroutine ...           yes  (flush)
Checking for the 'fdate' subroutine ...           yes  (fdate)
Checking for the 'secnds' function ...            yes  (secnds)
Checking for the 'date' subroutine ...            no
Checking for the 'time' subroutine ...            no
Checking for the 'etime' function ...             yes  (etime)
Checking for the 'lnblnk' function ...            yes
Checking for the 'hostnm' function ...            yes  (hostnm)
Testing if hostnm works ...                       yes  (returns login01.sanam)
Checking for the 'lstat' function ...             yes
Checking if lstat works ...                       yes
Checking if inquire works on directories ...      yes
Checking for record length ...                    4
Checking for the endianess of the machine ...     little endian
Checking for integer*8 ...                        yes
Checking for integer*2 ...                        yes

Looking for available C compilers ...             found: gcc cc c89

Input C compiler:                                 [gcc] /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/gcc
Input C compiler flags to use:                    [-O2 -fPIC]
Checking for fortran name mangling scheme ...     C compilation fails
failed to determine

Input path to EGSnrc HEN_HOUSE directory:         [/home/aabuhaimed/EGSnrc/HEN_HOUSE]
Choose a configuration name:                      [linux.conf]

Using HEN_HOUSE          = /home/aabuhaimed/EGSnrc/HEN_HOUSE
      configuration file = linux.conf
      configuration name = linux

Creating lib/linux directory ...                  OK
Creating config file linux.conf ...               OK
Creating machine.macros ...                       OK
Creating machine.f ...                            OK
Creating machine.mortran ...                      OK
Creating bin directory ...                        OK
Creating bin/linux directory ...                  OK
Creating log directory ...                        OK
Compiling mortran3 ...                            OK
Compiling pegs4 ...                               OK
Compiling beam_build ...                          OK
Compiling beamdp ...                              OK
Compiling ctcreate ...                            Skipping (no C compiler)
Compiling statdose ...                            OK
Compiling readphsp ...                            OK
Compiling dosxyz_show ...                         Skipping (no C compiler)
Compiling addphsp ...                             OK

Looking for installed C++ compilers ...           OK

Found the following C++ compilers in your search path:
    g++

Input C++ compiler:                               [g++]: /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/g++

Determining Fortran libraries for /mnt/apps/spack/opt/spack/linux-centos7-sandybridge/gcc-4.8.5/gcc-10.2.0-3mz7fbwnsw6y47vss3r5zam6l4er5z75/bin/g++ linking ...OK

Using the following compiler/linker switches for creating/linking against
dynamic shared objects (DSO, also known as shared library or DLL), where
$(abs_dso) or $(ABS_DSO) below will be replaced with the absolute path to the
EGSnrc DSO directory at compile/link time:

1) Optimization options:                          -O2 -mtune=native
2) Generation of position independent code:       -fPIC
3) Preprocessor defines:
4) Flag for creating shared libraries:            -shared
5) Output/dlopen library:                         -o $@
6) DSO path encoded in the executable:            -L$(abs_dso) -Wl,-rpath,$(abs_dso)
7) Linking against library some_lib:              -lsome_lib
8) Fortran libraries needed by C++ linker:        -lgfortran -lquadmath

Input option to change, or enter to proceed:

Creating C++ config file ...                      OK
Building the IAEA phase space library ...         Failed
Building the EGSnrc C++ class library ...         Failed

These settings did not work out. You may edit the source code
(in case you can see where the problem is when building the C++ libraries
from the configure.log file) and/or try different compiler/linker options.

Do you want to retry? (yes/no)                    no
Adding C++ make variables to configuration ...    OK

EGSnrc system configuration log saved in:
/home/aabuhaimed/EGSnrc/HEN_HOUSE/log/configure-linux.log

###############################################################################

The EGSnrc basic installation is complete.

Every user who wants to use the system must now run the following script to
specify the directory to keep EGSnrc user codes and set various useful
environment variables and aliases:

/home/aabuhaimed/EGSnrc/HEN_HOUSE/scripts/finalize_egs_foruser

###############################################################################

You are logged in as aabuhaimed.

This script can now launch 'finalize_egs_foruser' to proceed with the
installation of the EGSnrc user area for aabuhaimed.

Do you want to finalize for aabuhaimed? (yes/no): yes


###############################################################################
finalize_egs_foruser
###############################################################################

Copyright (C) 2015 National Research Council Canada

This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. See LICENCE file for
details or http://www.gnu.org/licenses/agpl.txt

###############################################################################

You can exit this script at any time by typing Ctrl-C.

Press enter to continue.

Choose a directory for your user codes:           [/home/aabuhaimed/EGSnrc/egs_home]

Creating egs_home ...                             OK
Creating bin directory ...                        OK
Creating bin/linux directory ...                  OK
Creating pegs4 directory ...                      OK
Creating pegs4/data directory ...                 OK
Creating pegs4/inputs directory ...               OK
Creating pegs4/density directory ...              OK
Creating beamnrc directory ...                    OK
Creating beamnrc/spec_modules directory ...       OK

Copying user codes to EGS_HOME area ...
    Copying cavity ...                            OK
    Copying cavrznrc ...                          OK
    Copying cavsphnrc ...                         OK
    Copying dosrznrc ...                          OK
    Copying dosxyznrc ...                         OK
    Copying edknrc ...                            OK
    Copying egs_app ...                           OK
    Copying egs_cbct ...                          OK
    Copying egs_chamber ...                       OK
    Copying egs_fac ...                           OK
    Copying egs_kerma ...                         OK
    Copying egs_phd ...                           OK
    Copying examin ...                            OK
    Copying flurznrc ...                          OK
    Copying g ...                                 OK
    Copying ranlux_test ...                       OK
    Copying ranmar_test ...                       OK
    Copying sprrznrc ...                          OK
    Copying tutor1 ...                            OK
    Copying tutor2 ...                            OK
    Copying tutor2pp ...                          OK
    Copying tutor3 ...                            OK
    Copying tutor4 ...                            OK
    Copying tutor5 ...                            OK
    Copying tutor6 ...                            OK
    Copying tutor7 ...                            OK
    Copying tutor7pp ...                          OK

Copying BEAMnrc examples .module files ...
    Copying EX10MeVe.module ...                   OK
    Copying EX16MVp.module ...                    OK
    Copying EXphantom.module ...                  OK
    Copying EXslabs.module ...                    OK

You may now compile user codes. Please select:
    1. Compile all
    2. Compile selected
    3. Compile none (default)

Choose 1 (all), 2 (some) or 3 (none):             [3] 1
    Compiling cavity ...                          Skipping (no egs++ installation)
    Compiling cavrznrc ...                        failed
    Compiling cavsphnrc ...                       OK
    Compiling dosrznrc ...                        failed
    Compiling dosxyznrc ...                       failed
    Compiling edknrc ...                          OK
    Compiling egs_app ...                         Skipping (no egs++ installation)
    Compiling egs_cbct ...                        Skipping (no egs++ installation)
    Compiling egs_chamber ...                     Skipping (no egs++ installation)
    Compiling egs_fac ...                         Skipping (no egs++ installation)
    Compiling egs_kerma ...                       Skipping (no egs++ installation)
    Compiling egs_phd ...                         Skipping (no egs++ installation)
    Compiling examin ...                          OK
    Compiling flurznrc ...                        failed
    Compiling g ...                               OK
    Compiling ranlux_test ...                     OK
    Compiling ranmar_test ...                     OK
    Compiling sprrznrc ...                        failed
    Compiling tutor1 ...                          OK
    Compiling tutor2 ...                          OK
    Compiling tutor2pp ...                        Skipping (no egs++ installation)
    Compiling tutor3 ...                          OK
    Compiling tutor4 ...                          OK
    Compiling tutor5 ...                          OK
    Compiling tutor6 ...                          OK
    Compiling tutor7 ...                          OK
    Compiling tutor7pp ...                        Skipping (no egs++ installation)

EGSnrc user configuration log saved in:
/home/aabuhaimed/EGSnrc/HEN_HOUSE//log/configure-linux-aabuhaimed.log

###############################################################################

The EGSnrc configuration for aabuhaimed is ALMOST complete ...

EGSnrc requires various environment variables and aliases to be defined.
Typically you add these definitions to your shell resource file located in
your home directory, to ensure the EGSnrc environment is properly set up
every time you log in.

Your default shell is /bin/bash
Add the following statements to your .bashrc file:

export EGS_HOME=/home/aabuhaimed/EGSnrc/egs_home/
export EGS_CONFIG=/home/aabuhaimed/EGSnrc/HEN_HOUSE/specs/linux.conf
source /home/aabuhaimed/EGSnrc/HEN_HOUSE/scripts/egsnrc_bashrc_additions

###############################################################################

[rtownson]

We're not yet compatible with the latest compilers. Please try gcc 7.5 or earlier.

[crcrewso]

We're going to need to fix this. Getting gcc below 8 is going to become difficult in the near future on some reasonable distros.

[crcrewso]

I've tried compilers up through 9 without issue. But the compilers have always been at /bin/* or similar. I'm wondering if there's something going on with the paths to your compiler executables.

[Abdullah-Abuhaimed]

Thank you @rtownson and @crcrewso for your responses, I will submit a request to the grid administrator to install gcc 7.5 and give it a try.

I have run the configuration script with gcc 8.3 in the same gird and had the same issue posted above. However, I have managed to configure EGSnrc successfully in my laptop with gcc 9.3 without any issue. It seems to me that there is an issue in the link between the configuration script and the module which is loaded by the user, i.e. a path issue, the gcc is not in the /user/bin directory. The c and g++ compilers are loaded, but they cannot be found during the configuration process. So it seems the issue is not related to the gcc version, EGSnrc works and runs in my laptop with no issue.

[ftessier]

@Abdullah-Abuhaimed do you have any update on this? Were you successful with gcc 7.5?