[Wien] Query regarding wien2k_scratch directory
Gavin Abo
gabo13279 at gmail.com
Sun Apr 28 21:27:59 CEST 2024
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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