[Wien] Query regarding wien2k_scratch directory
shamik chakrabarti
shamik15041981 at gmail.com
Mon Apr 29 20:19:23 CEST 2024
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,
>>>>>>
>>>>> _______________________________________________
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>>
>
>
> --
> 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
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