Frequently asked questions about usage of computers.
New jobs won't be accepted. Please be careful not only on the CPU usage but also on the disk usage.
In case group CPU points run out, jobs of that group will be removed after 24+ hours of that points exceedance.
We don't have interactive or debug queue.
You can build and test software on the frontend nodes (ccfep*, ccgpup, ccgpuv), where parallel make (e.g. make -j 12) or MPI program run (e.g. mpirun -np 12 ...) is allowed.
However, there are some performance limitations, which are intentionally employed, on those frontend nodes.
Please don't try production runs or long benchmark jobs on the frontend nodes.
CPU points will be used on ccfep* and ccgpuv according to the actual CPU usage. (If you just login and do nothing, virtually CPU points won't be consumed.)
To login to GPU equipped frontend nodes (ccgpup or ccgpuv), you first login to ccfep* and then "ssh" to ccgpup/ccgpuv.
No additional settings are required if you can login to ccfep*.
CPU/GPU limitation is basically determined from the initially assigned points. The actual values can be found in this table (right columns).
Current limitation can be shown by "jobinfo -q PN -c" command (do not add -l options in this case).
Here are the example. Blue- and red-colored "****" parts in "RunLim" row will show the max available CPUs/GPUs for you and your group, respectively.
[user@ccfep* ~]$ jobinfo -q PN -c
-----+------+---------------------------+-------------------------
Queue|Job |User(***) Group(***) |Total
Name |Status|CPUs,GPU/Jobs CPUs,GPU/Jobs| CPUs,GPUs/Jobs(Usr,Grp)
-----+------+---------------------------+-------------------------
PN |RunLim|****, **/- ****, **/- | xxxxx, xxx/- ( -, -)
|Run | x, x/x x, x/x | xxxxx, xxx/xxxx(xxx,xxx)
|Queue | x, x/x x, x/x | xxxxx, xxx/xxxx(xxx,xxx)
|Hold | x, x/x x, x/x | xxxxx, xxx/xxxx(xxx,xxx)
|Exit | x, x/x x, x/x | x, x/x ( x, x)
|Total | x, x/x x, x/x |xxxxxx,xxxx/xxxx(xxx,xxx)
-----+------+---------------------------+-------------------------
There are two types of limitations; user and group limitations.
Per user limitation can be assigned by the representative of the group at resource limit page.
If you have trouble in accessing from Japan, please check this page (need to login).
If you want to login from outside Japan, you need to submit an application form available in this page.
The applicants are basically required to have a valid academic affiliation in Japan and an account of RCCS; login of oversea collaborators to RCCS is generally not allowed.
You can use csh (tcsh), bash, or zsh as a login shell. This setting can be modified only via the center web page. To modify the setting, click "My account" item in the left pane first. (That item won't be shown if you are not logged in.) Then, click "Edit" tab in that page. You can choose your login shell using the combobox in that page. After the choice of the login shell, make sure to click "Save" button located below to save the modified setting.
It might take a time to untill the new setting becomes active. If the modification is not applied for more than a day, please contact us.
Once settings of multiple revisions of g16 are loaded, g16 job might die immediately.
Output example:
Entering Gaussian System, Link 0=/local/apl/lx/g16????/g16/._.g16
Initial command:
/local/apl/lx/g16****/g16/l1.exe "/work/users/***/********.cccms1/Gau-66921.inp" -scrdir="/work/users/***/********.cccms1/"
sh: /local/apl/lx/g16***/g16/l1.exe: Permission denied
Typically, this happens when configuration files are loaded both in the default setting files (such as .cshrc or .bashrc) and in the job script. You may need to modify either of default setting file or job script to solve this problem.
On the other hand, a single setting file can be loaded safely multiple times.
Also, you might (not always) be able to run Gaussian successfully after loading setting files of multiple Gaussian verisons (g09 and g16). It is not recommended, though.
There are some reports that Gaussian "Freq" calculations crash due to the memory shortage even though the available memory size is increased. In these case, *reduction* of available memory size could solve the problem, according to the reports. If you have tourble with this issue, this workaround maybe worth trying.
You need to load setting file before running formchk. If you want to convert checkpoint file from g16 output from LX queue, you need to run the following command. Please note that the setting file name depends on your login shell.
csh (tcsh):
$ source /local/apl/lx/g16/g16/bsd/g16.login
bash or zsh:
$ source /local/apl/lx/g16/g16/bsd/g16.profile
If you are using different version of Gaussian or queue, please replace the directory names above to the corresponding ones.
If you load one of gaussian modules (environment modules), corresponding version of formchk will be available.
If the requested version of python or the library is provided by the distribution, we can install them. However, we recommend you to build Anaconda environment in your home directory, because Anaconda covers wider area of the python applications/libraries used in academic science than the package set provided by the distribution.
We also prepared some Anaconda environments. Links to their usage page can be found at package program list page.
In some rare cases upon system troubles, modifications to files would be ignored at first glance.
This is generally caused by the mishandled file cache.
If you met this unlucky event, please check it carefully according to the following procedure.
If you find a suspicous file, please report the hostname and the file location to us: ccadm[at]draco.ims.ac.jp.
We will clear the file cache of that host. (This is because normal users cannot do this operation.)
You can fix it by yourself by file manipulation (not recommended, though).
If you try to fix, please make backup before the file manipulation.
On the other hand, files can be broken due to a storage trouble. "ls -l" might return the following type of output in some case. (This might happen upon file creation stage. Already existing file would not experience this type of trouble.)
ls: cannot access (file name): No such file or directory
-????????? ? ? ? ? ? (file name)
Unfortunately, this file is completely broken. All you can do for this file is just to remove.
You may need to employ "unlink" command instead of standard "rm" command to remove this file.
We prepared some samples in this page.
You can find some explanations in our manual. The sample scripts for each applications (/local/apl/lx/(name)/samples) may also be worth to check.
Please fill the following items and send it to ccadm[at]draco.ims.ac.jp.
Permission denied (publickey)
Permission denied (publickey,hostbased).
Private and public keys don't match or the public key is not registered. This message may be shown if the private key is not correctly prepared or specified.
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,hostbased).
This message will be shown if the private key is not correctly specified.
ssh:connect:Network is unreachable
ssh:connect:Host is unreachable
These messages will be shown if the network setting is incorrect or connection route to RCCS is not available due to some netowrk errors.
ssh:connect:Connection refused
ssh:connect:Connection timed out
RCCS service is temporary stopped for maintenance or some troubles. Or, the connection is refused accrording to the rules described below.
ssh_exchange_identification: Connection closed by remote host
Server unexpectedly closed network connection
Network failure happens or connection is refused according to the rules described below.
If the connection can't be establised successfully, adding verbose option to your ssh software will give you some useful information/messages. For example, if you are using "ssh" command on the terminal (maybe on Mac and Linux), verbose messages can be enabled by adding -v option.