FLUKA installation - Error: Failed dependencies libstdc++.so.6

ealemany · 15 June 2023 22:26

Hello,

I have a server with CentOS 7. Most of the users on the server need gcc version 4.8.
I installed from source (with --disable-multilib prefix for 64-bit OS) gcc-13.1.0 in /tmp directoy.
I edited the .bashrc file for the user who need a newer gcc version to point to the gcc-13 location.

I also installed

centos-release-scl-rh
devtoolset-9-toolchain
devtoolset-9-gcc-gfortran devtoolset-9-gcc-c++

When I checked the ggc and the gfortran version, I can see

gcc (GCC) 13.1.0
GNU Fortran (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)

I downloaded the recommended binaray package - fluka-4-3.3.x86-Linux-gfor9.x86_64.rpm

When i run rpm -ivh fluka-4-3.3.x86-Linux-gfor9.x86_64.rpm

I have the following errors:

error: Failed dependencies:
libstdc++.so.6(CXXABI_1.3.8)(64bit) is needed by fluka-4-3.3.x86_64
libstdc++.so.6(CXXABI_1.3.9)(64bit) is needed by fluka-4-3.3.x86_64
libstdc++.so.6(GLIBCXX_3.4.21)(64bit) is needed by fluka-4-3.3.x86_64

I checked the CXXABI version and noticed I did not have the right version

CXXABI_1.3
CXXABI_1.3.1
CXXABI_1.3.2
CXXABI_1.3.3
CXXABI_1.3.4
CXXABI_1.3.5
CXXABI_1.3.6
CXXABI_1.3.7
CXXABI_TM_1

I copied the /libstdc++.so.6 file from the gcc-13 installation location /tmp/gcc/usr/local/lib64/libstdc++.so.6 to /usr/lib64. Now I can see the newest version.

CXXABI_1.3
CXXABI_1.3.1
CXXABI_1.3.2
CXXABI_1.3.3
CXXABI_1.3.4
CXXABI_1.3.5
CXXABI_1.3.6
CXXABI_1.3.7
CXXABI_1.3.8
CXXABI_1.3.9
CXXABI_1.3.10
CXXABI_1.3.11
CXXABI_1.3.12
CXXABI_1.3.13
CXXABI_1.3.14
CXXABI_TM_1
CXXABI_FLOAT128
CXXABI_1.3
CXXABI_1.3.11
CXXABI_1.3.2
CXXABI_1.3.6
CXXABI_FLOAT128
CXXABI_1.3.12
CXXABI_1.3.9
CXXABI_1.3.1
CXXABI_1.3.5
CXXABI_1.3.8
CXXABI_1.3.13
CXXABI_1.3.4
CXXABI_TM_1
CXXABI_1.3.7
CXXABI_1.3.14
CXXABI_1.3.10
CXXABI_1.3.3

But when I tried to run the installation again i have the same error message.

error: Failed dependencies:
libstdc++.so.6(CXXABI_1.3.8)(64bit) is needed by fluka-4-3.3.x86_64
libstdc++.so.6(CXXABI_1.3.9)(64bit) is needed by fluka-4-3.3.x86_64
libstdc++.so.6(GLIBCXX_3.4.21)(64bit) is needed by fluka-4-3.3.x86_64

I am not a FLUKA user just a Sys Admin. I would greatly appreciate any tips and advice you can give me.

Thank you in advance for your help.

horvathd · 16 June 2023 06:15

Dear Eric,

please make sure that the version number of g++ and gfortran are the same. The FLUKA package compiled with gfortran 9 works with any gcc version from 8 to 13.

The fix probably would be to compile gcc with g++ and gfortran together.

Cheers,
David

NTB · 16 June 2023 08:02

Hi,
Having the devtoolset-9 installed, you can do everything inside a shell by invoking the command:
“scl enable devtoolset-9 bash”
The Bash shell should now have the right environment to install fluka using rpm.
The user must execute fluka (providing the relevant path) after devtoolset-9 is launched with the same command.
I hope it helps.
NTB

ealemany · 16 June 2023 16:23

Dear David,

Thank you for your advice. I checked to make sure the version number of g++ and gfortran are the same. This is the command I ran.

[root@mt-manager ~]# scl enable devtoolset-9 bash
[root@mt-manager ~]# g++ --version
g++ (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 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.

[root@mt-manager ~]# gfortran --version
GNU Fortran (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 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.

Unfortunately, I still have the libstdc++.so.6 error.

I understand the role of gcc, g++ and gfortran but I do not have experience in those programming language. I am very new at this.

Thank you for your help.

Best wishes,
Eric

ealemany · 16 June 2023 16:38

Hi Nunzio,

Thank you for your message. Indeed, I invoke scl enable devtoolset-9 bash and can confirm that the Bash shell is in the right environment to install Fluka using rpm. To make sure that I am doing it right this is what I do:

[root@mt-manager ~]# scl enable devtoolset-9 bash
[root@mt-manager ~]# gfortran --version
GNU Fortran (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 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.

[root@mt-manager ~]# g++ --version
g++ (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 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.

[root@mt-manager ~]# gcc --version
gcc (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)
Copyright (C) 2019 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.


[root@mt-manager ~]# rpm -ivh fluka-4-3.3.x86-Linux-gfor9.x86_64.rpm
error: Failed dependencies:
	libstdc++.so.6(CXXABI_1.3.8)(64bit) is needed by fluka-4-3.3.x86_64
	libstdc++.so.6(CXXABI_1.3.9)(64bit) is needed by fluka-4-3.3.x86_64
	libstdc++.so.6(GLIBCXX_3.4.21)(64bit) is needed by fluka-4-3.3.x86_64
[root@mt-manager ~]#

As I mentioned to David Horvath, I understand the role of gcc, g++ and gfortran but I do not have experience in those programming language. I am very new at this.

Thank you for your help.

Best wishes.
Eric

NTB · 16 June 2023 18:13

Hi Eric,
You do not need particular skills to compile FLUKA.
Just as a last guess, you can try this:

download the fluka-4-3.3.x86-Linux-gfor9.tgz package from the fluka website.
decompress it in a convenient directory.
check if the Zlib (compression-decompression library used by FLUKA to access low-energy neutron nuclear data) is already installed. Otherwise, install it using yum (sorry, I forget the name of the specific CENTOS package).
launch devtoolset-9 and goto to the directory fluka4-43.3/src, and type “make” to compile and link FLUKA.

This procedure works on our servers at CRESCO-ENEA. In the tgz package, the main FLUKA routines are present as a pre-compiled object, and the users’ routines are in the form of Fortran and C/C++ source code. Consequently, after compilation of the source code, it links all compiled and pre-compiled objects in a FLUKA executable using the libstdc++.so already installed in the system.
If the compilation fails, you must check carefully the installation of devtoolset-9 to see if there is any missing piece.
I hope again it helps
NTB

ealemany · 19 June 2023 14:49

Hi Nunzio,

I followed your instructions and as far as I can tell it worked. The only “warning” message I saw during the compilation (make) was:

`usbrea.f:378:132:

  378 |      &                ERR = 6750 )
      |                                                                                                                                    1
Warning: The STATUS specified in OPEN statement at (1) is ‘NEW’ and no FILE specifier is present`

Other than that there was no error messages.

Is there anything I need to tell the users before they start using FLUKA. I am just a Sys Admin and they are the smart ones to use the software.

Thank you for your help.

Best wishes,
Eric

NTB · 19 June 2023 15:12

Hi Eric,
Mission accomplished!
Now it’s the user’s turn to test FLUKA with their simulations.
Remember that each FLUKA job must be launched within the devtoolset-9 shell, and it is also mandatory each time they want to compile and link their user routine to the fluka main.
Have a nice day
NTB

ealemany · 19 June 2023 15:39

Hi Nunzio,

Perfect then!. Thank you so much for your help. And yes, I will make sure to remind users to launch the devtoolset-9 shell.

Have a great week.

Best wishes,
Eric