Important notice about the reallocation error of libm on linux system when installing xpdfsuite

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Songsheng Tao

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Mar 1, 2021, 2:12:48 PMMar 1
to diffpy-users
Dear all:

I am a Ph. D. student in Billinge group. Recently, we received report about the reallocation error when users are installing the xpdfsuite. The symptom is like:

``Python27/bin/python: relocation error: /home/<user>/xPDFsuite/Python27/bin/../lib/libm.so.6: symbol __get_cpu_features version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference``

It is because that the libm in Python27/lib need libc in linux systme lib and the system lib has a newer version of libc and this caused the the symbol not found error.

Deleting the libm in the Python27/lib and making xPDFsuite use the libm in the system will solve the problem. The steps are shown below:

1. Open a termianl and change the directory to xPDFsuite.

``cd /home/<user>/xPDFsuite``

In this example, the path is ``/home/<user>/xPDFsuite``. Please change the path according to where the xPDFsuite folder is on your system.

2. Delete libm.so.6 in the Python27/lib.

``rm Python27/lib/libm.so.6``

3. Run the python installation.

``Python27/bin/python install.py``

4. Add the alias for xpdfsuite. Use your favorite text editor to open the ``~/.bashrc`` file on your system and add the following line in that file and save the file and reopen the terminal.

``alias xpdfsuite='/home/<user>/xPDFsuite/xPDFsuite'``

Please change the ``/home/<user>/xPDFsuite`` to the path to xPDFsuite on your system.. In this case, we create an alias named "xpdfsuite" and you can run ``xpdfsuite`` in the terminal to open the software. You may also change the name to your favorite name.

Sincerely,
Songsheng

Simon Billinge

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Mar 1, 2021, 2:20:28 PMMar 1
to diffpy...@googlegroups.com
Thanks Songsheng,

Everyone, Just a note that there is nothing you need to do unless you see this error message when you are installing xPDFsuite on some linux distributions.  It should not happen in most cases, but if you encounter this error, Songsheng lays out the workaround.  We are working on a more permanent solution too.

S

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Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory
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