[Wien] Query regarding wien2k_scratch directory
shamik chakrabarti
shamik15041981 at gmail.com
Mon Apr 29 20:10:22 CEST 2024
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
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