FAQ (general & Molecular Science)

Only the registered Email address is necessary to reset password or/and register public keys on this website. The three-character user id is required when you modify your information on this website after the first login or when you login to the supercomputer system.

When you failed to receive password reset Email, there may be something wrong with the entered or registered address. Please contact us if you can't receive the email. For the initially registered Email addresses of group members, the representative person can see them on the "Members" tab ("組織表ダウンロード" button; sorry, English UI is not yet available for this part...) in the page of your application on NOUS. Even when the user account field was left blank when you submitted the application, the members' correct user accounts should be available there.

Alternatively, if there are already logged in users in your group, they can see the three-character account names of the group members at "List group members" page on this website (login required). You may also be able to check whether you are registered in the correct group.
 

It is not possible to change your email address on this website after the submission of your application for this FY. Please enter your new Email address in the form available in "Member Management" page and then send us in the manner indicated on that page.

For the Email addresses of group members registered upon submission, the representative person can see them on the "Members" tab ("組織表ダウンロード" button) in the page of your application on NOUS.
 

If you want to login from outside Japan, you need to submit an application. The template file can be downloaded from this page. The applicants are required to have a valid academic affiliation in Japan and an account of RCCS; login of oversea collaborators to RCCS is generally not allowed.

If you have trouble in accessing from Japan, please check documents in quick start guide page.

Remote host name and user name

The host name is "ccfep.ims.ac.jp". The user name is a 3-character account (English letters only or English letters + numbers) assigned by RCCS.

Registration of public key(s)

You need to register your public key on this website. Please check this page for information on how to register.

In case permissions of ssh related files/directories are wrong

In case you accidentally change the permissions of your home directory or ~/.ssh, ~/.ssh/authorized_keys, you can no longer login. If a login session remains, please fix the permissions using that. If you have already logged out, please contact us. We will fix the permissions.

Connection closed immediately / Connection timed out

This situation may occur during system troubles. Please check the information on the top page of our website first. Also, you will not be able to login during maintenance. Please wait until the maintenance is finished.

If you receive a "Permission denied" message, your public key or user name may not be correct. Please review your settings by referring to the Quick Start Guide.

If you are waiting for a long time without any response, or if a message such as "Connection timed out" or "Connection closed" is displayed immediately, network connection might be blocked by something like firewall. In this case, please contact the person in charge of your network environment.
 

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.

It will take up to 10 minutes before the system updates the usage status (i.e. before the update of showlim command output). For example, suppose you notice that you have exceeded your disk usage and immediately delete the file. Still you need to wait up to 10 minutes before the your new submission is allowed.
 

CPU points of a job are calculated from the elapsed time (execution time) of the job. For example, if the job's time limit (walltime) is 24 hours and the elapsed time is 1 hour, CPU points for 1 hour will be used.
 

The amount of available memory for a job is proportional to the number of the CPU cores allocated to that job. For largemem jobs, you can use about 8 GB (~7.45 GiB) per core. For other types of jobs, you can use about 2 GB (~1.86 GiB) per core.

When you employ 64 CPU cores (ncpus=64), you can use ~512 GB for jobtype=largemem jobs and ~128 GB for other jobs, respectively. If a large amount of memory is needed but not so many CPU cores, it is still necessary to employ many CPU cores.
 

Please check this page.
 

You can build and test software on the login servers (ccfep*). Parallelized build of programs (e.g. make -j 12) and MPI program tests (e.g. mpirun -np 12 ...) are also allowed. For GPU software, please use ccgpu (do "ssh ccgpu" on ccfep to login).

However, there are some performance limitations, which are intentionally employed, on those login servers. Please don't try production runs or long benchmark jobs. CPU points will be used on ccfep* according to the actual CPU usage. (If you are just logged in and do nothing, CPU points won't be consumed.)

Interactive jobs are not available to all the users for now. If you want to use interactive jobs, please ask us. Please note that there are some additional restrictions (walltime, number of CPUs/GPUs for example) for interactive jobs.
 

You can apply for additional CPU points or/and disk space. Details can be found at this page. Please be careful about limitations.
 

You can use csh (tcsh), bash, or zsh as a login shell. This setting can be modified only at this RCCS web site. To modify the setting, click "My account" item at the top pf page. (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 combo box. After the choice of the login shell, make sure to click "Save" button at the bottom of the page.

It may take up to 20 minutes for the changes to take effect. If the modification is not applied for more than a day, please contact us. 
 

Major reasons why your jobs won't run are listed below. If you meet exceptional/unknown cases, feel free to contact us.

Not enough resources (CPU, GPU) available

You can check the status of available resources in this website or using "jobinfo -s" command. Once login to this site and go to the top page, you will find the status on the right column of the page. There can be enough space for other types of jobs. Switching jobtype (if possible) might be a good idea in this case.
 

My job won't run even though enough computational resources are available.

First, run jobinfo command to check the reason why your jobs won't run. You can find the reason at the rightmost column of the output. Major reasons are:

• (cpu), (gpu), (cpu/gpu): not enough cpu/gpu available
• (group): due to the group limit
• (long): walltime too long (once a job began to run, that must be finished before the next maintenance)
• (other): some other reason. This also displayed for just submitted jobs; please wait for a while in this case.
  • Please also try without "-c" option. "jobinfo -c" sometimes can't show the correct reason due to the insufficient information from the queuing system.

In case of (group), you or members of your group are using large amount of resources. Please ask corresponding person to do something. FYI, representative person or authorized member(s) can limit the resource usage of each member at the resource limit page.

On the other hand, in case of (long), you may need to shorten the walltime of your job or wait until the end of next maintenance. (NOTE: queued jobs won't be deleted upon monthly maintenance.)

My jobtype=core jobs won't run even though enough computational resources are available.

Multinode jobs are not allowed for jobtype=core jobs; a job must reside on single node. Even when there are so many free CPU cores for jobtype=core in total, those free cores are often scattered among nodes and there may be not enough space for your large jobtype=core jobs. You might want to use 64 cores (jobtype=vnode) in some cases; jobtype=vnode may have room for your job. Also, for ncpus=46-63 jobs, switching to ncpus=64 is more advantageous in terms of CPU points (64 cores => 45 points/hour, 46 cores => 46 points / hour, 63 cores => 63 points / hour).
 

This error will happen when output of .bashrc is large. For example, if setvars.sh of Intel oneAPI is loaded in .bashrc, this message may appear. There are some ways to avoid this error.

• discard output to /dev/null
• allow output only if $PS1 exists (interactive case)
• move the corresponding lines to ~/.bash_profile
   

You need to load setting file before running formchk. If you want to convert checkpoint file, you need to run the following command. Please note that the setting file name depends on your login shell.

bash or zsh:

$ source /apl/gaussian/16c02/g16/bsd/g16.profile

csh (tcsh):

$ source /apl/gaussian/16c02/g16/bsd/g16.login

(You can ignore "PYTHONPATH: Undefined variable." message. Setting is correctly loaded and formchk is available in this case.) 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 becomes available.
 

Some python versions and libraries are available via yum. Please ask us if you need them. Or you can install packages by yourself using pip3 command with --user option (see example below). Packages will be installed in your home directory (probably under ~/.local).

$ pip3 install numpy --user

You can also use pyenv or/and miniforge. Anaconda is also a very good solution if there is no problem about license. If you are planning to use GPUs, we recommend to use conda environment such as miniforge. Runtime library for GPUs (cudatoolkit) can be installed easily with conda.

Miniforge environments prepared by RCCS are also available. You can load them by sourcing /apl/conda/(date)/conda_init.sh or /apl/conda/(date)/conda_init.csh.
 

In the current system, we don't provide Intel Compilers to users. If you need them, please install Intel oneAPI Base Toolkit and HPC Toolkit into your directory.
https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit.html (Base Toolkit)
https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit.html (HPC Toolkit)
(These toolkits can be installed free of charge. However, there are restrictions upon redistribution.)
 

Following applications require an application for use or registration.

• ORCA => User registration on the official site and e-mail to RCCS required.
• GRRM23 => An application for use required.
• Open OnDemand => You need to register a password on this website.
• Crystal => An application for use required (see the bottom of the page).
• AlphaFold3 => Model parameters required.

We prepared some samples in this page. You can find some explanations in our manual. The sample scripts for each applications (/apl/(name)/(version)/samples) may also be worth to check.
 

Please fill the following items and send it to rccs-admin[at]ims.ac.jp (please replace [at] by @).

• Software name and version that you want to use
• Overview of the software and its feature
• Why that software is necessary in RCCS supercomputer
• URL of the official website