Does loading R_packages/4.3.1 load R? Which version? Is it allways the same version? Does it always take around the same time?
| Project | Setting | R module version | Real loading time |
|---|---|---|---|
| Rackham | SSH | 4.3.1 | 0m0.758s |
| sens2016001 | SSH | Unknown | Unknown |
| sens2023598 | SSH | 4.3.1 | 6m1.265s |
| sens2023598 | Website | 4.3.1 | 6m20.234s |
| sens2017625 | SSH | 4.3.1 | 6m4.584s |
| sens2017625 | Website, interactive session | 4.3.1 | 7m41.433s |
| sens2017625 | SSH, interactive session | 4.3.1 | 7m13.111s |
This rejects H1.
For details, see module_load.md
I created this post at 2024-12-06 11:06:
When I do time module load R_packages/4.3.1 I get load times that differ by a factor of >100x between Rackham (less then 1 second) and Bianca (more then 6 minutes). Is there a reason for this? Exact timings and what I did can be found at https://github.com/UPPMAX/ticket_304069/blob/master/module_load.md#answers
This timing is indeed off! The sysexperts are working on it.
- Does loading
R_packages/4.3.1load theRmodule? - If yes, which version?
- How long does it take?
| Project | Setting | R module version | Real loading time |
|---|---|---|---|
| Rackham | SSH | 4.3.1 | 0m0.758s |
| sens2016001 | SSH | Unknown | Unknown |
| sens2023598 | SSH | 4.3.1 | 6m1.265s |
| sens2023598 | Website | 4.3.1 | 6m20.234s |
| sens2017625 | SSH | 4.3.1 | 6m4.584s |
| sens2017625 | Website, interactive session | 4.3.1 | 7m41.433s |
| sens2017625 | SSH, interactive session | 4.3.1 | 7m13.111s |
[richel@sens2017625-b4 ~]$ time module load R_packages/4.3.1
R_packages/4.3.1: Note that loading some spatial analysis packages, especially geo-related packages, might
R_packages/4.3.1: require you to load additional modules prior to use. monocle3 is such a package. See
R_packages/4.3.1: 'module help R_packages/4.3.1'
R_packages/4.3.1: The RStudio packages pane is disabled when loading this module, due to RStudio slowdowns
R_packages/4.3.1: because there are >20000 available packages. *All packages are still available.* For
R_packages/4.3.1: more information and instructions to re-enable the packages pane (not recommended) see
R_packages/4.3.1: 'module help R_packages/4.3.1'
^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B
real 7m13.111s
user 0m0.906s
sys 0m1.416s
Took 7m41.433 seconds
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Sun Nov 10 19:17:03 2024 from vpnpool188-114.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
###################d####q####w############x#####x################x##############x###
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:23:44 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
##########################################x##########################x#########
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:33:03 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
########################################################################g#####
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:45:32 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
#############################################d#############################x###
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:52:05 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
###########################################s########x##########x#x############x###
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 08:08:11 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
######################x#####x##########x######x#######################x###########
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 08:18:57 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
###########################x##################################################
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 08:28:20 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
#############################################################################
ssh: connect to host sens2016001-bianca.uppmax.uu.se port 22: No route to host
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2016001@bianca.uppmax.uu.se
richel-sens2016001@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 08:39:34 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
###############################################################d#####
I wanted to do the things below, but I gave up as the node does not start.
time module load R_packages/4.3.1
module list- R version: 4.3.1
- Time: 6 minutes
[richel@sens2023598-bianca ~]$
[richel@sens2023598-bianca ~]$ module list
^C/usr/bin/lua: /usr/share/lmod/lmod/libexec/../tools/capture.lua:75: interrupted!
stack traceback:
[C]: in function 'read'
/usr/share/lmod/lmod/libexec/../tools/capture.lua:75: in function 'capture'
/usr/share/lmod/lmod/libexec/../tools/TermWidth.lua:52: in function 'l_askSystem'
/usr/share/lmod/lmod/libexec/../tools/TermWidth.lua:86: in function 'TermWidth'
/usr/share/lmod/lmod/libexec/cmdfuncs.lua:375: in function 'cmd'
/usr/share/lmod/lmod/libexec/lmod:513: in function 'main'
/usr/share/lmod/lmod/libexec/lmod:584: in main chunk
[C]: ?
Connection to sens2023598-bianca.uppmax.uu.se closed.
Connection to bianca.uppmax.uu.se closed.
richel@richel-N141CU:~$ ssh richel-sens2023598@bianca.uppmax.uu.se
richel-sens2023598@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:42:45 2024 from vpnpool189-175.anst.uu.se
****************************************************************************
* Login node up and running. Redirecting now! *
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
richel@sens2023598-bianca.uppmax.uu.se's password:
Permission denied, please try again.
richel@sens2023598-bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:32:32 2024 from 172.18.144.254
_ _ ____ ____ __ __ _ __ __
| | | | _ \| _ \| \/ | / \ \ \/ / | System: sens2023598-bianca
| | | | |_) | |_) | |\/| | / _ \ \ / | User: richel
| |_| | __/| __/| | | |/ ___ \ / \ |
\___/|_| |_| |_| |_/_/ \_\/_/\_\ |
###############################################################################
User Guides: http://www.uppmax.uu.se/support/user-guides
FAQ: http://www.uppmax.uu.se/support/faq
Write to support@uppmax.uu.se, if you have questions or comments.
[richel@sens2023598-bianca ~]$ time module load R_packages/4.3.1
R_packages/4.3.1: Note that loading some spatial analysis packages, especially geo-related packages, might
R_packages/4.3.1: require you to load additional modules prior to use. monocle3 is such a package. See
R_packages/4.3.1: 'module help R_packages/4.3.1'
R_packages/4.3.1: The RStudio packages pane is disabled when loading this module, due to RStudio slowdowns
R_packages/4.3.1: because there are >20000 available packages. *All packages are still available.* For
R_packages/4.3.1: more information and instructions to re-enable the packages pane (not recommended) see
R_packages/4.3.1: 'module help R_packages/4.3.1'
real 6m1.265s
user 0m1.194s
sys 0m1.599s
[richel@sens2023598-bianca ~]$ time module list
Currently Loaded Modules:
1) uppmax 6) texlive/2023-08-14 11) bzip2/1.0.8
2) gcc/12.3.0 7) libcurl/7.85.0 12) zlib/1.2.12
3) java/OpenJDK_17+35 8) readline/6.2-11 13) R/4.3.1
4) cairo/1.17.4 9) libicu/5.2-4 14) R_packages/4.3.1
5) texinfo/6.8 10) xz/5.2.6
real 0m31.461s
user 0m0.125s
sys 0m0.196s
[richel@sens2023598-bianca ~]$
- R version: 4.3.1
- Time: 6 minutes
richel@richel-N141CU:~$ ssh richel-sens2017625@bianca.uppmax.uu.se
richel-sens2017625@bianca.uppmax.uu.se's password:
Last login: Fri Dec 6 07:42:33 2024 from vpnpool189-175.anst.uu.se
############################################################################
# Login node NOT up! Boot initiated. Just wait for prompt #
# or login again later. This can take from 2 to 6 minutes #
############################################################################
****************************************************************************
* Notice! No second factor if you use password. *
* If you use ssh keys, you can get rid of this (second) prompt. *
****************************************************************************
##################################################################
richel@sens2017625-bianca.uppmax.uu.se's password:
_ _ ____ ____ __ __ _ __ __
| | | | _ \| _ \| \/ | / \ \ \/ / | System: sens2017625-bianca
| | | | |_) | |_) | |\/| | / _ \ \ / | User: richel
| |_| | __/| __/| | | |/ ___ \ / \ |
\___/|_| |_| |_| |_/_/ \_\/_/\_\ |
###############################################################################
User Guides: http://www.uppmax.uu.se/support/user-guides
FAQ: http://www.uppmax.uu.se/support/faq
Write to support@uppmax.uu.se, if you have questions or comments.
[richel@sens2017625-bianca ~]$ time module load R_packages/4.3.1
R_packages/4.3.1: Note that loading some spatial analysis packages, especially geo-related packages, might
R_packages/4.3.1: require you to load additional modules prior to use. monocle3 is such a package. See
R_packages/4.3.1: 'module help R_packages/4.3.1'
R_packages/4.3.1: The RStudio packages pane is disabled when loading this module, due to RStudio slowdowns
R_packages/4.3.1: because there are >20000 available packages. *All packages are still available.* For
R_packages/4.3.1: more information and instructions to re-enable the packages pane (not recommended) see
R_packages/4.3.1: 'module help R_packages/4.3.1'
real 6m4.584s
user 0m1.193s
sys 0m1.634s
[richel@sens2017625-bianca ~]$ time module list
Currently Loaded Modules:
1) uppmax 6) texlive/2023-08-14 11) bzip2/1.0.8
2) gcc/12.3.0 7) libcurl/7.85.0 12) zlib/1.2.12
3) java/OpenJDK_17+35 8) readline/6.2-11 13) R/4.3.1
4) cairo/1.17.4 9) libicu/5.2-4 14) R_packages/4.3.1
5) texinfo/6.8 10) xz/5.2.6
real 0m31.708s
user 0m0.121s
sys 0m0.146s
[richel@sens2017625-bianca ~]$ ls
bianca codium_is_here.txt Desktop R start_interactive.sh
bin core.13061 plot.R sens2017625 video_demo.txt
[richel@sens2017625-bianca ~]$ time ls
bianca codium_is_here.txt Desktop R start_interactive.sh
bin core.13061 plot.R sens2017625 video_demo.txt
real 0m20.971s
user 0m0.008s
sys 0m0.075s
[richel@sens2017625-bianca ~]$ ll
total 36
drwxrwsr-x 2 richel richel 4096 Jan 9 2024 bianca
drwx--S--- 2 richel richel 4096 Apr 20 2023 bin
-rw-rw-r-- 1 richel richel 4 Dec 13 2023 codium_is_here.txt
-rw------- 1 richel richel 10200 Aug 8 2023 core.13061
drwxrwsr-x 2 richel richel 4096 Jun 14 2023 Desktop
-rw-rw-r-- 1 richel richel 0 Dec 13 2023 plot.R
drwxrwsr-x 4 richel richel 4096 Jun 8 2023 R
lrwxrwxrwx 1 richel richel 18 Jul 13 2023 sens2017625 -> /proj/sens2017625/
-rwxrwxr-x 1 richel richel 49 Dec 13 2023 start_interactive.sh
-rw-rw-r-- 1 richel richel 0 Dec 13 2023 video_demo.txt
Note core.13061
[richel@rackham2 ~]$ time module load R_packages/4.3.1
R_packages/4.3.1: Note that loading some spatial analysis packages, especially geo-related packages, might
R_packages/4.3.1: require you to load additional modules prior to use. monocle3 is such a package. See
R_packages/4.3.1: 'module help R_packages/4.3.1'
R_packages/4.3.1: The RStudio packages pane is disabled when loading this module, due to RStudio slowdowns
R_packages/4.3.1: because there are >20000 available packages. *All packages are still available.* For
R_packages/4.3.1: more information and instructions to re-enable the packages pane (not recommended) see
R_packages/4.3.1: 'module help R_packages/4.3.1'
real 0m0.758s
user 0m0.377s
sys 0m0.140s
[richel@rackham2 ~]$ module list
Currently Loaded Modules:
1) uppmax 6) texlive/2023-08-14 11) bzip2/1.0.8
2) gcc/12.3.0 7) libcurl/7.85.0 12) zlib/1.2.12
3) java/OpenJDK_17+35 8) readline/6.2-11 13) R/4.3.1
4) cairo/1.17.4 9) libicu/5.2-4 14) R_packages/4.3.1
5) texinfo/6.8 10) xz/5.2.6