[Wien] Query regarding wien2k_scratch directory
Laurence Marks
laurence.marks at gmail.com
Mon Apr 29 20:26:05 CEST 2024
You *really* should be doing your own searching on this rather than posting
here.
https://askubuntu.com/questions/1487330/what-is-a-tracker3-folder-inside-home-cache-is-it-safe
___
Professor Laurence Marks (Laurie)
Walter P Murphy Professor Emeritus
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi
On Tue, Apr 30, 2024, 02:20 shamik chakrabarti <shamik15041981 at gmail.com>
wrote:
> Also, it is found that *tracker 3 contains all the 12 GB space, *should I
> remove this folder or the files inside it?
>
> On Mon, 29 Apr 2024 at 23:40, shamik chakrabarti <shamik15041981 at gmail.com>
> wrote:
>
>> Dear Prof. Gavin,
>>
>> After invoking all the commands you have listed I have come to know
>> that *.cache *folder contains 12 GB of space. .cache folder contains the
>> followings;
>>
>> event-sound-cache.tdb.bb916188e665483abe367841b820014a.x86_64-pc-linux-gnu
>> gstreamer-1.0 pip ubuntu-report
>> evolution
>> ibus thumbnails update-manager-core
>> fontconfig
>> ibus-table thunderbird yelp
>> gnome-desktop-thumbnailer
>> mesa_shader_cache tracker3
>>
>> Is anything removable from this folder to recover the space?
>>
>> with regards,
>>
>> On Mon, 29 Apr 2024 at 00:58, Gavin Abo <gabo13279 at gmail.com> wrote:
>>
>>> The operating system /var log files I typically would not remove.
>>> Before attempting to remove any of them, I would ask the operating system
>>> experts if it would be safe to do so. For Ubuntu for example, I think
>>> those experts would be over in the Ubuntu forums at [1].
>>>
>>> The 15 GB is quite large such that I wouldn't expect the operating
>>> system with default logging to instantly cause that but get larger more
>>> gradually over time.
>>>
>>> The du command [2] you might find helpful. Below is an example.
>>>
>>> First, I looked at the directories in the root folder for seeing which
>>> ones were using the most drive space:
>>>
>>> username at computername:~$ sudo du --exclude=/proc --exclude=/run -csh /*
>>> 0 /bin
>>> 197M /boot
>>> 4.0K /cdrom
>>> 0 /dev
>>> 14M /etc
>>> 2.6G /home
>>> 0 /lib
>>> 0 /lib32
>>> 0 /lib64
>>> 0 /libx32
>>> 16K /lost+found
>>> 44K /media
>>> 4.0K /mnt
>>> 4.0K /opt
>>> 56K /root
>>> 0 /sbin
>>> 3.7G /snap
>>> 4.0K /srv
>>> 2.1G /swapfile
>>> 0 /sys
>>> 164K /tmp
>>> 6.6G /usr
>>> 3.2G /var
>>> 19G total
>>>
>>> In my case, I'm storing my WIEN2k calculations under
>>> /home/username/wiendata and have my SCRATCH set to the case folders (with
>>> ./) that I put in that directory:
>>> username at computername:~$ grep wiendata ~/.bashrc
>>> alias cdw="cd /home/username/wiendata"
>>> export W2WEB_CASE_BASEDIR=/home/username/wiendata
>>> username at computername:~$ grep SCRATCH ~/.bashrc
>>> export SCRATCH=./
>>>
>>> I can check the space of just the /home directory with:
>>>
>>> username at computername:~$ du -csh /home
>>> 2.6G /home
>>> 2.6G total
>>>
>>> I see 2.6 GB of space is being used.
>>>
>>> I check what I have under my home directory:
>>>
>>> username at computername:~$ ls /home
>>> username
>>>
>>> There I see I only have one user account, which is named username.
>>>
>>> I check how much space is being used by username:
>>>
>>> username at computername:~$ du -csh /home/username
>>> 2.6G /home/username
>>> 2.6G total
>>>
>>> Next, I check under /home/username to see what the 2.6 GB consists of:
>>>
>>> username at computername:~$ cd /home/username/
>>> username at computername:~$ du -csh * .[^.]*
>>> 4.0K Desktop
>>> 4.0K Documents
>>> 4.0K Downloads
>>> 4.0K Music
>>> 4.0K Pictures
>>> 4.0K Public
>>> 124M snap
>>> 4.0K Templates
>>> 4.0K Videos
>>> 1.5G WIEN2k
>>> 180M wiendata
>>> 4.0K .bash_history
>>> 4.0K .bash_logout
>>> 4.0K .bashrc
>>> 130M .cache
>>> 176K .config
>>> 12K .gnupg
>>> 697M .local
>>> 4.0K .profile
>>> 4.0K .ssh
>>> 0 .sudo_as_admin_successful
>>> 4.0K .wget-hsts
>>> 2.6G total
>>>
>>> I see my WIEN2k installation is using 1.5 GB of the 2.6 GB used. My
>>> wiendata is currently only using 180 MB.
>>>
>>> Looking in my wiendata folder, I currently only have one case
>>> calculation named Al:
>>>
>>> username at computername:~$ ls /home/username/wiendata/
>>> Al
>>>
>>> I find it is taking the entire 180 MB:
>>>
>>> username at computername:~$ du -csh /home/username/wiendata/*
>>> 180M /home/username/wiendata/Al
>>> 180M total
>>>
>>> To display how much is used under the /home directory in MB, I use:
>>>
>>> username at computername:~$ du -csh --block-size=M /home
>>> 2624M /home
>>> 2624M total
>>>
>>> I want to move the Al directory from the computer to my USB connected
>>> external storage drive similar to what you described. First though, since
>>> my storage drive has a Windows NTFS partition, I have to rename the :log
>>> file to avoid a transfer error and I chose to name it log.txt:
>>>
>>> username at computername:~$ mv /home/username/wiendata/Al/:log
>>> /home/username/wiendata/Al/log.txt
>>>
>>> Creating an archive (.tar) or compressed file (.zip) of the Al directory
>>> would have been an alternate solution that would not have required renaming
>>> of the :log file.
>>>
>>> I transferred the entire directory to my USB connected flash drive
>>> (mounted at /media/username/1A50-FE2F/Al) using a mv command in the bash
>>> terminal:
>>>
>>> username at computername:~$ mv /home/username/wiendata/Al
>>> /media/username/1A50-FE2F/Al
>>>
>>> I rechecked wiendata directory after that and see the Al file is gone
>>> (i.e., was transferred successfully):
>>>
>>> username at computername:~$ ls /home/username/wiendata/
>>>
>>> I check the space of /home again:
>>>
>>> username at computername:~$ du -csh --block-size=M /home
>>> 2445M /home
>>> 2445M total
>>>
>>> I see that the used /home space dropped 179 MB (= 2624M - 2445M). The 1
>>> MB could be due to rounding error or other active processes going on the
>>> system taking it, but I was essentially able to get an entire 180 MB of
>>> free space back for this case as expected.
>>> [1] https://ubuntuforums.org/
>>> [2]
>>> https://www.tecmint.com/check-linux-disk-usage-of-files-and-directories/
>>>
>>> On 4/27/2024 11:23 AM, shamik chakrabarti wrote:
>>>
>>> Sir, also it is showing 139 Mb however my device space get decreased by
>>> almost 15 GB
>>>
>>> On Sat, 27 Apr 2024 at 22:51, shamik chakrabarti <
>>> shamik15041981 at gmail.com> wrote:
>>>
>>>> total 139M
>>>> 4.0K drwxr-x--- 28 shamik shamik 4.0K Apr 26 23:48 .
>>>> ...
>>>> 4.0K drwxrwxr-x 2 shamik shamik 4.0K Jun 26 2023 WIEN2k
>>>>
>>>> On Sat, 27 Apr 2024 at 22:48, Peter Blaha <peter.blaha at tuwien.ac.at>
>>>> wrote:
>>>>
>>>>> ls -alsh
>>>>>
>>>>>
>>>>> Am 27.04.2024 um 17:57 schrieb shamik chakrabarti:
>>>>>
>>>>> Dear Prof. Gavin,
>>>>>
>>>>> Yes, wien2k is installed under the /home directory. I
>>>>> have also checked /var. there are log files as mentioned in your reference
>>>>> [1]. In this regard, which files should I remove to recover the lost spaces?
>>>>>
>>>>> with regards,
>>>>>
>>>>> On Sat, 27 Apr 2024 at 17:42, Gavin Abo <gabo13279 at gmail.com> wrote:
>>>>>
>>>>>> If your WIEN2k cases are located somewhere under the /home directory,
>>>>>> is this the directory you are seeing the space increase in?
>>>>>>
>>>>>> If your looking at the space of the entire storage drive before and
>>>>>> after the calculation, another possibility is the increase could be due to
>>>>>> normal usage logging by the operating system. So, if its the /var you are
>>>>>> seeing increase after the calculation, it could potentially be due to that
>>>>>> as log files could be stored there as seen for example at [1].
>>>>>> [1]
>>>>>> https://ubuntu.com/tutorials/viewing-and-monitoring-log-files#2-log-files-locations
>>>>>>
>>>>>> Kind Regards,
>>>>>> Gavin
>>>>>> WIEN2k user
>>>>>>
>>>>>> On 4/26/2024 10:52 PM, shamik chakrabarti wrote:
>>>>>>
>>>>>> In that case, after deleting the case directory, the space in hd of
>>>>>> Linux should be recovered. But the space is decreasing every time, I ran
>>>>>> some calculations and after copying delete the whole directory.
>>>>>>
>>>>>> On Sat, 27 Apr 2024, 01:48 Tomas Kana, <kana at seznam.cz> wrote:
>>>>>>
>>>>>>> The dot and slash ./ means your current directory
>>>>>>>
>>>>>>>
>>>>>>> Dear Sir,
>>>>>>>
>>>>>>> After echo $SCRATCH the output is: ./
>>>>>>>
>>>>>>>
>>>>>>> Any comments
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, 26 Apr 2024 at 22:14, Peter Blaha <peter.blaha at tuwien.ac.at>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> During userconfig you have specified a SCRATCH directory. Only
>>>>>>> you can know what you did there.
>>>>>>>
>>>>>>> PS: echo $SCRATCH will tell you, what you specified.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Am 26.04.2024 um 13:30 schrieb shamik
>>>>>>> chakrabarti:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear Wien2k users,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> After running calculations I am saving
>>>>>>> the data in external hdd while deleting the same from
>>>>>>> linux.
>>>>>>> However, at each time, after deleting data, I have found
>>>>>>> that
>>>>>>> some amount of spaces are not recovered. Wien2k is saving
>>>>>>> some
>>>>>>> files in Linux which I am not able to delete.
>>>>>>>
>>>>>>> My query is where are those extra files are stored? Whether
>>>>>>> there is some directory called as _scratch but then I am
>>>>>>> not
>>>>>>> able to find it either?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Any response is eagerly awaited.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> with regards,
>>>>>>>
>>>>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>> SEARCH the MAILING-LIST at:
>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>
>>
>>
>> --
>> Dr. Shamik Chakrabarti
>> Research Fellow
>> Department of Physics
>> Indian Institute of Technology Patna
>> Bihta-801103
>> Patna
>> Bihar, India
>>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
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