This is a page of "How to" solve some computer problems that may happen.

P = problem; S = solution

P: (2016.03.10) A new FLEX user cannot receive e-mail.

S: Don't forget to restart dovecot and postfix after creating the user

$ sudo service dovecot restart
$ sudo service postfix restart

P: (2015.08.06) Sometimes CPU RAM disc is occupied by unused memory and it isn't deleted or moved automatically. (Particularly in the case we calculated by Quantum espresso in local disc.)

S: We can free up by following command.

We can check our current memory usage using this command:

$ watch -n 1 free -m


$ watch -n 1 cat /proc/meminfo

We can free up unused memory under Ubuntu/Linux Mint using this command:

$ sudo sysctl -w vm.drop_caches=3


$ sudo sync && echo 3 | sudo tee /proc/sys/vm/drop_caches

Please check this site, too:

P: (2014.10.17) SSH Error with GSSAPI unsupported options

When we login to TUBE systems, the following message appears:

/etc/ssh/ssh_config line 53: Unsupported option "gssapiauthentication"
/etc/ssh/ssh_config line 54: Unsupported option "gssapidelegatecredentials"

S: Modify /etc/ssh/ssh_config of FLEX

Give comment sign to the following lines (or remove them completely)

#    GSSAPIAuthentication yes
#    GSSAPIDelegateCredentials no

Try again to login to TUBE systems.

P: (2014.10.14) HTML helper mode by emacs does not work for updating the timestamp

S: The hhmts code should be in one line and with a proper spacing in order for emacs to change the HTML time-stamp automatically.


<!-- hhmts start --> Last modified: Tue Oct 14 16:58:36 JST 2014 <!-- hhmts end  -->

is a CORRECT syntax.


<!-- hhmts start -->
Last modified: Tue Oct 14 16:58:36 JST 2014
<!-- hhmts end -->

is a FALSE syntax.

P: (2014.8.22) DVI file does not show figures after compiling latex files.

S: Do not use any additional option in graphicx package

  • In the past, people usually add:
  • In the current latex system, excluding any options is sufficient:

P: (2014.8.20) Thunderbird connection to flex does not work.

S: Edit /etc/dovecot/conf.d/20-imap.conf


mail_max_userip_connections = 10 

and then

sudo service dovecot restart

P: (2014.8.19) NFS in new FLEX Ubuntu 14.04 is very slow

S: This is a known bug for the latest ubuntu. We should fix nfs-common and blacklist kerberos configuration.

  • In /etc/default/nfs-common:
    should be modified to be
  • In /etc/modprobe.d/blacklist.conf add the following line
    # Blacklist rpcsec_gss_krb5 kernel module; needed for quick NFSv4 mounts
    blacklist rpcsec_gss_krb5
  • Restart nfs daemon:
    $ sudo service nfs-kernel-server restart

Check also this reference:

P: (2014.8.18) Samba sever cannot be accessed in the new FLEX (Ubuntu 14.04)

S: We found that the location of passdb.tdb should be different to the old FLEX

  • In old FLEX, passdb.tdb is put under
  • In new FLEX, passdb.tdb should instead be put under
  • After putting passdb.tdb in the correct location, don't forget to restart the samba services:
    # sudo service smbd restart
    # sudo service nmbd restart

P: (2014.8.14) E-mail sent through aliasing system (all, slab, etc) always repeats itself around every half an hour

S: Check the routing policy is correct

  • Check /etc/hosts is set correctly
  • Execute again /root/ on old FLEX and /root/ on new FLEX
  • If the problem still exists, restart both old FLEX and new FLEX and execute again above scripts.
  • Make sure other computers do not share the same hostname.

P: (2014.8.13) Evince does not work well on Ubuntu 14.02

S: Do the following way

sudo ln -s /etc/apparmor.d/usr.bin.evince /etc/apparmor.d/disable 
sudo /etc/init.d/apparmor restart 
and add
export NO_AT_BRIDGE=1
to /etc/environment

P: (2014.8.13) How to change mouse focusing policy.

S: System --> Preferences --> Window then find a panel "Behaviour" and click: "Select windows when the mouse moves over them"

P: (2014.8.13) How to change desktop language

S: - for all users: edit /etc/default/locale and add:

LANG = "ja_JP.UTF-8" 

I've done this for new FLEX - for a particular user (corresponding user should do by himself): edit ~/.dmrc and add under [Desktop] section:


(If we want English, just change above line by



P: How to zip-file in win8.1 with password which is compatible with all users unzip programs:

S: Download and install 7-zip

 1. Download the 7-zip installer for your computer from  Run the program and install 7-zip to your computer.
 2. Choosing your files.
 3. Right-click on items and choosing 7-Zip, then Add to archive.
 4. choose your format from Archive format `zip`.
 5. Enter password.
 6. Finally, OK to create the compressed archive.

P: (2014.08.04) FLEX can be accessed from Xlaunch (local), but global component such as website and e-mail seem doesn't work

S: If you have such a symptom, probably iptable was accidentally modified. We should recover the routing rule to a normal way.

  • Run the following script:
    $ sudo /root/

P: (2014.07.24) Xming is no longer good for Windows 8.1

S: Install Vcxsrv, which is a clone of Xming, and remove Xming itself.

  • Download Vcxsrv from the following:
  • After installation, do these steps:
    • Open Xlaunch.
    • Choose "One large window" and press Next.
    • Select "Open sesson via xdmcp" and press Next.
    • Connect to host: and press Next.
    • Give the following additional parameters for Vcxsrv:
      -from <your_working_ip_address>
      for example (please change the address, the following is Nugraha's example):
    • Push Next button, Save Configuration, and Finish.

P: (2014.01.17) NIS in tube 60 does not work, although NFS works

S: Activate ypbind with the following command

# sysv-rc-conf ypbind on 
# reboot

P: (2013.10.24) X-windows does not work, cannot connect to Flex using X-windows (Xming, NX, etc.)

S: restart X-windows service in Flex

#sudo service lightdm restart

P:(2013.08.26) E-mail does not work after shutting down the Flex

S: restart dovecot and postfix

#service dovecot start
#service dovecot stop
#service dovecot restart
#sudo /etc/init.d/postfix restart

P:(2013.06.05) how to customize GDM login screen

S: using ubuntu-tweak

Install ubuntu-tweak

 #sudo add-apt-repository ppa:tualatrix/ppa
 #sudo apt-get update
 #sudo apt-get install ubuntu-tweak

Launch ubuntu-tweak from terminal and customize the login screen

P: (2013.06.03) xdvi doesn't put period and comma correctly when reading Japanese documents.

S: Check a tutorial created by other people

Install xdvi-ja

# apt-get install xdvik-ja

Font map file: /etc/texmf/vfontmap.d/

Do the following:

# cd /etc/texmf/vfontmap.d/
# mv
# mv
# mv 

Next, check the fc-list the name of the Japanese font to use.

$ fc-list | grep Takao
Takao P??,TakaoPMincho:style=Regular
Takao P????,TakaoPGothic:style=Regular

Add the following lines to a file (create new if not exist) under the directory /etc/texmf/vfontmap.d/

       rml  JIS-H      % ASCII pTeX
       rmlv JIS-V      % ASCII pTeX
       dm   JIS-H      % NTT jTeX
       rml-jis  JIS-H  % ptex-jisfonts
       gbm  JIS-H      % ASCII pTeX
       gbmv JIS-V      % ASCII pTeX
       dg   JIS-H      % NTT jTeX
       gbm-jis  JIS-H  % ptex-jisfonts

Finally, update the registration information of the font

# update-vfontmap

P: (2012.10.02) How to remove Ubuntu welcome notes

Welcome to Ubuntu 11.10 (GNU/Linux 3.0.0-25-generic x86_64)

 * Documentation:
 New release '12.04 LTS' available.
 Run 'do-release-upgrade' to upgrade to it.
 *** System restart required ***

S: Please check /etc/update-motd.d/ folder

Then change the permission

 sudo chmod 600 * 

P: (2012.09.26) Warning: File `Makefile' has modification time 38 s in the future

warning: Clock skew detected. Your build may be incomplete. Such warning appears in TUBE50

S: TUBE50 clock is not synchronized to

P: (2012.09.25)"yes" command appears every time we restart TUBE50

S: check file /etc/default/nfs-common

  • before:
    NEED_IDMAPD= yes
  • after:
    important to note: <space> has meaning to separate the variable in sh script.

P: (2012.08.29) Changing default text editor

S: run this command:

sudo update-alternatives --config editor

P: (2012.03.29) Segmentation fault when login tube

S: run this command /rsaito/bin/no-passwd

Then press Enter anytime the statement appears

P: (2010.04.29) set-pathname-coding-system function does not exists in new xemacs lisp which existed in flex.

P: (2010.01.19) Managing ntp

S: ntp and ntpdate package have to be configured in some tricky ways

  • ntp.conf file
    [root@tube40 ~]# emacs /etc/ntp.conf
    The /etc/ntp.conf file is the main configuration file for Linux NTP in which we place the IP addresses of the servers we want to use. Here we only use one server:
    server    # A stratum 1 server at
    #server     # A stratum 2 server at
    We have to restart the NTP process every time we make a change to the configuration file for the changes to take effect on the running process.
  • To get NTP configured to start at boot, use the line:
    [root@tube40 ~]# chkconfig ntpd on
  • To start, stop and restart NTP after booting, follow these examples:
    [root@tube40 ~]# /etc/init.d/ntpd start
    [root@tube40 ~]# /etc/init.d/ntpd stop
    [root@tube40 ~]# /etc/init.d/ntpd restart
  • For the synchronization, ntpd should be stopped and ntpdate should be run at least three times, then ntpd can be run again:
    [root@tube40 ~]# /etc/init.d/ntpd stop
    Shutting down ntpd:                                        [  OK  ]
    [root@tube40 ~]# /usr/sbin/ntpdate -u
    19 Jan 16:11:08 ntpdate[23079]: adjust time server offset 0.016601 sec
    [root@tube40 ~]# /usr/sbin/ntpdate -u
    19 Jan 16:11:09 ntpdate[23080]: adjust time server offset 0.015737 sec
    [root@tube40 ~]# /usr/sbin/ntpdate -u
    19 Jan 16:11:13 ntpdate[23081]: adjust time server offset 0.014081 sec
    [root@tube40 ~]# /etc/init.d/ntpd start
    Starting ntpd:                                             [  OK  ]

P: (2010.01.13) The problem of 2010.1.6 is solved but response is slow.

S: The problem is due to the fact that /etc/mtab is on root (not snapshot)

Since we do not know what is the process of mount the file. we can not change mtab to snapshot. For a moment, we force mount /home1 and /rsaito on /tmp/home1, /tmp/rsaito

/etc/rc5.d/S28autofs stop
mkdir /tmp/home1
mkdir /tmp/rsaito
mount -n /tmp/home1
mount -n /tmp/rsaito


P: (2010.1.6) /rsaito is not automountd on PXE client.

S: edit and add flexS:/rsaito information on


P: (2009.10.10) Gnorm logout is slow for Xming etc.

This is a firewall problem of windows.

S: Open port 16001 tcp

control panel -> firewall -> add new port ->

Name Esound
Port 16001

P: (2009.07.17) Load average of FLEX is very high.

This is due to mounting problem again (mount NFS). After checking mount status, it is found that a network harddisk was not unmounted nicely before turning off.

S: Re-mount (turn on) the harddisk, and do some safety procedure.

  • check mount status:
    # mount
  • umount once (assuming mount point is /mnt/backup):
    # umount -f /mnt/backup
  • synchronize several times:
    # sync
    # sync
    # sync
  • check df or mount status again
  • if the harddisk has been nicely unmounted, then it is safe to turn it off.

P: (2009.07.02) Flex is unstable for logining or e-mails.

S: mount to tube:/home1-old was not allowed any more.

comment out one line in /etc/auto.misc 
# home1
./S28autofs forcerestart
I also delete in /etc/exports 
the requests from (nuguraha) (mahabubu)
and (furu).
exportfs -a
we also need to restart nfs
/etc/rc5.d/S60nfs restart

P: (2009.06.03) Today we were failed to run ether-wake command on new-PXE server/client machines using new Hub/router.

S: We manually turn those on and off. After that ether-wake (wake-on-Lan) command was successful.

P: PXE (network boot) is now installing 2009.5.1

S: finished. status PXE Server (Open)

P: We move /etc/passwd then we can not be root. No more even shutdown.

S: cntl-alt-del and reboot. Then when OS selection, push any arrow.

Then many selection of OS appears. Select one of OS, and press E. Then select kernel and press E again. Then you can edit the command for starting kernel and add "single" in the last of the command. Finally select "b" for booting and single user mode appears. Make /etc/passwd files and exit and runlevel 5 is recovers.

Even if we used NIS, we should not delete /etc/passwd /etc/group and /etc/shadow.

P: linux emacs ispell error (no language "eu") 2009.4.24

S: solved. "M-x ispell-change-dictionary" and select english

S: solved. Edit .emacs to add (setq ispell-dictionary "english")

P: How to update the files of remote to the files of local

S: solved. "rsync -avc -e ssh saito@remote:/home/saito/book09/ /rsaito/book09"

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Last-modified: 2016-03-10 (Thu) 02:11:59 (382d)