BwUniCluster2.0/Maintenance/2020-10: Difference between revisions

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The following changes are planned for the maintenance interval starting on 06.10.2020 (Tuesday) at 10 AM and ending on 13.10.2020 (Tuesday) at 10 AM.
The following changes have been introduced during the maintenance interval between 06.10.2020 (Tuesday) 10 AM and on 13.10.2020 (Tuesday) 10 AM.

With the maintenance the host key of the system has changed. Most SSH clients warn about this change or refuse to connect. Please follow the instructions of your SSH client to accept the following new host keys, depending on the algorithm your are using:

{|class="wikitable"
! Algorithm
! Hash (SHA256)
! Hash (MD5)
|-
|RSA
|p6Ion2YKZr5cnzf6L6DS1xGnIwnC1BhLbOEmDdp7FA0
|59:2a:67:44:4a:d7:89:6c:c0:0d:74:ba:3c:c4:63:6d
|-
|ECDSA
|k8l1JnfLf1y1Qi55IQmo11+/NZx06Rbze7akT5R7tE8
|85:d4:d9:97:e0:f0:43:30:6e:66:8e:d0:b6:9b:85:d1
|-
|ED25519
|yEe5nJ5hZZ1YbgieWr+phqRZKYbrV7zRe8OR3X03cn0
|42:d2:0d:ab:87:48:fc:1d:5d:b3:7c:bf:22:c3:5f:b7
|}


= Operating system =
= Operating system =


* The operating system version will be upgraded to Red Hat Enterprise Linux (RHEL) 8.2. We recommend to re-compile all applications after the upgrade.
* The operating system version was upgraded to ''Red Hat Enterprise Linux'' (RHEL) 8.2 (from 7.7.) . We recommend to re-compile all applications after the upgrade.


* The Linux kernel version will be upgraded to 4.18 (from 3.10).
* The ''Linux kernel'' version was be upgraded to 4.18 (from 3.10).


* The Mellanox OFED InfiniBand Stack will be upgraded to version 4.9 (from 4.7). If you maintain libraries which directly link against OFED libraried (e.g. MPI or PGAS libraries compiled in your $HOME directory) we recommend to re-compile these libraries after the upgrade.
* The ''Mellanox OFED'' InfiniBand Stack was upgraded to version 4.9 (from 4.7). If you maintain libraries which directly link against OFED libraried (e.g. MPI or PGAS libraries compiled in your $HOME directory) we recommend to re-compile these libraries after the upgrade.


= Compilers, Libaries and Runtime Environments =
= Compilers, Libaries and Runtime Environments =


* The ''GNU C Library'' (glibc) will be upgraded to version 2.28 (from 2.17). This version will no longer automatically print backtraces after stack checking failures due to security hardening, which might affect the debugging of applications.
* The ''GNU C Library'' (glibc) was upgraded to version 2.28 (from 2.17). This version no longer automatically prints backtraces after stack checking failures due to security hardening, which might affect the debugging of your applications.


* The default system compiler will be upgraded to ''GCC'' version 8.3.1 (from 4.8.5).
* The default system compiler was upgraded to ''GCC'' version 8.3.1 (from 4.8.5).


⚫
* The system ''Python'' version was upgraded to 3.6. If no other Python module is loaded, the ''python'' command now defaults to Python 3.6, while Python 2.7 can be still used with the ''python2'' command.
⚫
* The Intel compiler module versions will not change.


⚫
* The system ''Perl'' version was upgraded to 5.26 (from 5.16).
⚫
* The ''Clang'' 8 module will be removed and Clang 10 will be introduced. Clang 9 will continue to be available. Please note that the naming convention will change. While Clang 8 will still be available as compiler/clang/8, Clang 10 will be part of the compiler/llvm/10 module. This was necessary because LLVM has evolved into a compiler suite with many frontends (Clang, Flang, F18 etc.) and tools (LLDB), much like GCC.

⚫
* The ''PGI Compiler'' will be updated to version 20.7 (from 19.1). It includes the NVIDIA environment in version 11.0 (e.g. nvcc).

⚫
* The system ''Python'' version will be upgraded to 3.6. If no other Python module is loaded, the ''python'' command will default to Python 3.6, while Python 2.7 can be still used with the ''python2'' command.

⚫
* The system ''Perl'' version will be upgraded to 5.26.


= Development tools =
= Development tools =


* The default system version of the ''GNU Make'' build utility will be upgraded to 4.2.1. Please note the new ''--output-sync'' command line option that allows better debugging of parallel builds.
* The default system version of the ''GNU Make'' build utility was upgraded to 4.2.1 (from 3.82). Please note the new ''--output-sync'' command line option that allows better debugging of parallel builds.


* The default system version of the ''autotools'' package will be upgraded to 2.69. The "devel/autotools/2.69" software module is no longer necessary and will be removed.
* The default system version of the ''autotools'' package was upgraded to 2.69. The "devel/autotools/2.69" software module is no longer necessary and was removed.


* The default system version of the ''CMake'' build system will be upgraded to 3.11.
* The default system version of the ''CMake'' build system was upgraded to 3.11 (from 2.8.12.2).


* The default system version of the ''Git'' version control utility will be upgraded to 2.18.4. The "devel/git/2.18.4" software module is no longer necessary and will be removed.
* The default system version of the ''Git'' version control utility was upgraded to 2.18.4 (from 1.8.3.1). The "devel/git/2.18.4" software module is no longer necessary and was removed.


* Cent OS8's RPM now is case-insensitive, i.e. it will thread ''%VERSION%'' as ''%version'' followed by ''%'' -- this will lead to further errors; pre-defined RPM-macros should not be used in other contexts.
* Cent OS8's RPM tools are now case-insensitive, for example it will treat the macro ''%VERSION%'' as ''%version'' followed by a ''%'' sign. This will lead to further errors. Pre-defined RPM-macros like ''%version'' should therefore not be used in other contexts.


= Userspace tools =
= Userspace tools =
Line 41: Line 55:
* The ''screen'' utility is no longer be supported by Red Hat. The recommended replacement is ''tmux''.
* The ''screen'' utility is no longer be supported by Red Hat. The recommended replacement is ''tmux''.


== Software category: chem ==
= Software Modules =


Please not that the following list is not exhaustive.
⚫
* The default version of ''molden'' has been upgraded from 6.2 to 6.5

== Category: chem/ ==

⚫
* The default version of ''molden'' was upgraded to 6.5 (from 6.2).

== Category: compiler/ ==

⚫
* The Intel compiler module versions have not changed.

⚫
* The ''Clang'' 8 module was removed and Clang 10 was introduced. Clang 9 is still available. Please note that the naming convention changes starting with LLVM/Clang version 10. While Clang 9 is still available as ''compiler/clang/9'', Clang 10 is now part of the ''compiler/llvm/10'' module. This was necessary because LLVM has evolved into a compiler suite with many frontends (Clang, Flang, F18 etc.) and tools (LLDB), much like GCC, so it does no longer make sense to split LLVM and its compiler frontends into different modules.

⚫
* The ''PGI Compiler'' was updated to version 20.7 (from 19.1). It includes the NVIDIA CUDA environment in version 11.0 (e.g. nvcc)

== Category: math/ ==

* The ''R'' module (math/R/3.6.3) was rebuilt against the new operating system libraries. This should have no effect, but we recommend users to rebuild their private R packages as well.

* ''Matlab'' version R2020b was installed.

== Category: vis/ ==

* ''Blender'' 2.90.0 and 2.90.1 are now available.


= Batch system =
= Batch system =


* The Slurm version will be upgraded to version 20.02.5 (instead of 20.02.3).
* The ''Slurm'' version was upgraded to version 20.02.5 (instead of 20.02.3).


* The maximum total number of jobs of a single user in all queues (running and waiting) will be reduced to 100 (from 200).
* The maximum total number of jobs of a single user in all queues (running and waiting) was reduced to 100 (from 200).


= Storage =
= Storage =


* Mounting the LSDF will also be possible in the "single" queue.
* Mounting the LSDF is now also be possible in the "single" queue.


= Graphics stack =
= Graphics stack =


* The KDE Plasma desktop environment is no longer supported by Red Hat. ''start_vnc_desktop'' will default to GNOME 3.28 instead.
* The ''KDE Plasma'' desktop environment is no longer supported by Red Hat. ''start_vnc_desktop'' now defaults to GNOME 3.28 instead.

* The NVIDIA driver will be upgraded to the latest version available at the start of the maintenance interval.

= Containers =


* The NVIDIA driver was upgraded to version 450.51.06.
* Network Namespaces will be disabled due to security concerns.

Latest revision as of 12:49, 7 October 2022

The following changes have been introduced during the maintenance interval between 06.10.2020 (Tuesday) 10 AM and on 13.10.2020 (Tuesday) 10 AM.

With the maintenance the host key of the system has changed. Most SSH clients warn about this change or refuse to connect. Please follow the instructions of your SSH client to accept the following new host keys, depending on the algorithm your are using:

Algorithm Hash (SHA256) Hash (MD5)
RSA p6Ion2YKZr5cnzf6L6DS1xGnIwnC1BhLbOEmDdp7FA0 59:2a:67:44:4a:d7:89:6c:c0:0d:74:ba:3c:c4:63:6d
ECDSA k8l1JnfLf1y1Qi55IQmo11+/NZx06Rbze7akT5R7tE8 85:d4:d9:97:e0:f0:43:30:6e:66:8e:d0:b6:9b:85:d1
ED25519 yEe5nJ5hZZ1YbgieWr+phqRZKYbrV7zRe8OR3X03cn0 42:d2:0d:ab:87:48:fc:1d:5d:b3:7c:bf:22:c3:5f:b7

Operating system

  • The operating system version was upgraded to Red Hat Enterprise Linux (RHEL) 8.2 (from 7.7.) . We recommend to re-compile all applications after the upgrade.
  • The Linux kernel version was be upgraded to 4.18 (from 3.10).
  • The Mellanox OFED InfiniBand Stack was upgraded to version 4.9 (from 4.7). If you maintain libraries which directly link against OFED libraried (e.g. MPI or PGAS libraries compiled in your $HOME directory) we recommend to re-compile these libraries after the upgrade.

Compilers, Libaries and Runtime Environments

  • The GNU C Library (glibc) was upgraded to version 2.28 (from 2.17). This version no longer automatically prints backtraces after stack checking failures due to security hardening, which might affect the debugging of your applications.
  • The default system compiler was upgraded to GCC version 8.3.1 (from 4.8.5).
  • The system Python version was upgraded to 3.6. If no other Python module is loaded, the python command now defaults to Python 3.6, while Python 2.7 can be still used with the python2 command.
  • The system Perl version was upgraded to 5.26 (from 5.16).

Development tools

  • The default system version of the GNU Make build utility was upgraded to 4.2.1 (from 3.82). Please note the new --output-sync command line option that allows better debugging of parallel builds.
  • The default system version of the autotools package was upgraded to 2.69. The "devel/autotools/2.69" software module is no longer necessary and was removed.
  • The default system version of the CMake build system was upgraded to 3.11 (from 2.8.12.2).
  • The default system version of the Git version control utility was upgraded to 2.18.4 (from 1.8.3.1). The "devel/git/2.18.4" software module is no longer necessary and was removed.
  • Cent OS8's RPM tools are now case-insensitive, for example it will treat the macro %VERSION% as %version followed by a % sign. This will lead to further errors. Pre-defined RPM-macros like %version should therefore not be used in other contexts.

Userspace tools

  • The screen utility is no longer be supported by Red Hat. The recommended replacement is tmux.

Software Modules

Please not that the following list is not exhaustive.

Category: chem/

  • The default version of molden was upgraded to 6.5 (from 6.2).

Category: compiler/

  • The Intel compiler module versions have not changed.
  • The Clang 8 module was removed and Clang 10 was introduced. Clang 9 is still available. Please note that the naming convention changes starting with LLVM/Clang version 10. While Clang 9 is still available as compiler/clang/9, Clang 10 is now part of the compiler/llvm/10 module. This was necessary because LLVM has evolved into a compiler suite with many frontends (Clang, Flang, F18 etc.) and tools (LLDB), much like GCC, so it does no longer make sense to split LLVM and its compiler frontends into different modules.
  • The PGI Compiler was updated to version 20.7 (from 19.1). It includes the NVIDIA CUDA environment in version 11.0 (e.g. nvcc)

Category: math/

  • The R module (math/R/3.6.3) was rebuilt against the new operating system libraries. This should have no effect, but we recommend users to rebuild their private R packages as well.
  • Matlab version R2020b was installed.

Category: vis/

  • Blender 2.90.0 and 2.90.1 are now available.

Batch system

  • The Slurm version was upgraded to version 20.02.5 (instead of 20.02.3).
  • The maximum total number of jobs of a single user in all queues (running and waiting) was reduced to 100 (from 200).

Storage

  • Mounting the LSDF is now also be possible in the "single" queue.

Graphics stack

  • The KDE Plasma desktop environment is no longer supported by Red Hat. start_vnc_desktop now defaults to GNOME 3.28 instead.
  • The NVIDIA driver was upgraded to version 450.51.06.
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