The Challenge

“…aaaaand DONE!”

“Wow, amazing, 3 liters of beer! You got me, here you have your credits.” I leave the last one empty liter mug beside the other two and I pick up with a smooth move the golden coins my challenger is throwing me over the table. Not bad! But here it comes! I look around and I empty my lungs.

“BUUUUUUURP!”

My big burp is celebrated with clasps around our table. The challenge has gathered around us 15 expectant people, that I hope, will be generous on the payment, also.

“And now, just for the press, another one!” I burp again. This time, in a more musical tone. People laugh! That’s my business, to entertain them. I waive my hut. “If you like what you see, please tip me, I’m never tipsy enough!” More laughs. Unfortunately, not a lot, I need to make a note about prepare more my drinking jokes. But I wonder how long I will have until I start feeling the effects of what I just did. I look at the challenger. In his late 30’s, long hair, dressed correctly. I like his leather jacket. And he seems to be pretty comfortable here. Obviously he has money and he’s cute. Was he cute before I started to drink? Is he not staring at my tits right now?

“Sorry man, but I need to pee!” I manage to shout. He shouts also. “Of course, my lady! Do you need some help down there?” He smiles around. Is he a competitor? Laughs from the public, I hope good for me, not for him. Sometimes I’m surprised we live in the XXII century. But, also, this is, after all, not the Earth.

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Scipion 1.1 module on CentOS 7

After a long break of not writing at all, I will try to regularly make entries again. At least, one per day. One of software, one of fiction. Probably I will not manage, but today I’m going to try to follow the How to Install 1.1 bin instructions from the Scipion wiki.

I assume you already downloaded the binary, meaning you filled up the software request and so on. Since CentOS 7 is a SuSE flavor, previous to installation we should have a look to Installing dependencies for SuSE. It does have a specific section for Cent OS7. In my case, only java is missing, so I did install java on CentOS7.

As you know, we have modules, therefore I will try to use them. My firs blind install gave me an openmpi library error, so it will not be easy. After unzipping the package as suggested, and running the configuration (I don’t want to repeat what you have on the How to) the output is looking like this:

./scipion config --overwrite
Scipion v1.1 (2017-06-14) Balbino
>>>>> python /root/scipion/scipion/pyworkflow
/apps/pw_config.py "--overwrite"
* Creating backup:
/root/scipion/scipion/config/backups/scipion.conf.1502896067
* Creating configuration file: 
/root/scipion/scipion/config/scipion.conf
Please edit it to reflect the configuration of your system.

* Creating backup: 
/root/scipion/scipion/config/backups/protocols.conf.1502896067
* Creating configuration file: 
/root/scipion/scipion/config/protocols.conf
Please edit it to reflect the configuration of your system.

* Creating backup: 
/root/scipion/scipion/config/backups/hosts.conf.1502896067
* Creating configuration file: 
/root/scipion/scipion/config/hosts.conf
Please edit it to reflect the configuration of your system.

All the expected sections and options found in 
/root/.config/scipion/scipion.conf
Checking paths in /root/scipion/scipion/config/scipion.conf ...
All seems fine with /root/scipion/scipion/config/scipion.conf

Of course I overwrite the previous configuration, since my first compilation failed. The install help is offering you the chance to indeed install a lot of stuff:

./scipion install --help
[..some more stuff here..]
Available packages: 
([ ] not installed, [X] seems already installed)
 Gautomatch 0.53 [ ]
 Gctf 0.50 [ ] 1.06 [ ]
 bsoft 1.8.8 [ ] 1.9.0 [ ]
 chimera 1.10.1 [ ]
 cryoem 1.0 [ ]
 ctffind 3.6 [ ]
 ctffind4 4.0.15 [ ] 4.1.5 [ ] 4.1.8 [ ]
 dogpicker 0.2.1 [ ]
 eman 2.11 [ ] 2.12 [ ]
 ethan 1.2 [ ]
 frealign 9.07 [ ]
 gEMpicker 1.1 [ ]
 localrec 1.1.0 [ ] 1.2.0 [ ]
 mag_distortion 1.0.1 [ ]
 motioncor2 16.03.16 [ ] 16.10.19 [ ] 17.01.30 [ ]
 motioncorr 2.1 [ ]
 nma [ ]
 relion 1.3 [ ] 1.4 [ ] 1.4f [ ] 2.0 [ ]
 resmap 1.1.5s2 [ ]
 simple 2.1 [ ]
 spider 21.13 [ ]
 summovie 1.0.2 [ ]
 unblur 1.0.15 [ ] 1.0.2 [ ]

Our system is not clean, and most of the programs offered we have previously installed. I’m going to go for a flavorful of the suggested installation. More specifically

./scipion install bsoft-1.9.0 --no-xmipp

The goal is to get xmipp installed linked with scipion. In the scipion binary I downloaded xmipp comes compiled, so we are in principle done. Note that if you don’t install the program with the –no-xmipp tag, you will get the error `software/em/xmipp/external/imagej.tgz’ not found. Now, to make it beautiful, what I do is softlink the program we want in the software/em folder. Like this:

ln -s /usr/local/relion-1.4 software/em/relion-1.4

The possibility is officially given on this link. Therefore it should work. My scipion module looks at the end like this:

#%Module1.0##############################
## modules scipion-1.1
## modulefiles/scipion-1.1. scipion-1.1
##
proc ModulesHelp { } {
 global version modroot
 puts stderr "scipion-1.1 - sets scipion-1.1"
}
module-whatis "Sets the environment for using scipion-1.1"

# for Tcl script use only
set topdir /usr/local/scipion_v1.1
set version 1.1
set sys linux86
prepend-path PATH $topdir
module load python-2.7.13
module load mpi-2.1.0

With this module you may need to load the module of the program you want to use after loading the scipion module. I don’t know and I’m not going to test it. If I get a lot of complains, as usual, I will edit the post to let you know. So please come back from time to time 😉 .

Posted in bits, centos, linux, slurm | Leave a comment

Antikythera mechanism

I just realized I didn’t add a picture of the historical artifact. Here you have it.

mechanism_gearing_hr

I’m not going to insult your intelligence and add a wikipedia link. Just a couple of comments about: this one, together with the Phaistos Disc almost convinced me of  studying history instead of Physics. If only I had good memory for the dates…

Posted in dragons, new dreams, yellow earth | Leave a comment

Download Thunderbird emails as txt files

I’m still on holidays. Yes I am! Despite of the the tags of the post. But I can’t avoid thinking about what I need to do when I come back after my holidays. I’d love to have a law like the french right to disconnect but then, can I apply it if I’m not based in a certain place? And how can I disconnect my brain? Anyway, what I wanted to write down so I don’t forget it is how can I download as a txt file an email from my Thunderbird client.

The problem is the next. You have an email client for your corporative email address. That is already a supposition, since you may be a Microsoft Outlook person, or a gmail one. But let’s suppose you use Thunderbird. Then let’s suppose you have some kind of email quota (that we don’t have) or that you simply want to get the email content ordered by date on a specific folder, so you can copy them to a pendrive, or something like that. In my case, after managing doing what I want, I will try to build a database so I can order them by keywords, or by tags, and offer the result to a third person as a website. I may tell you about it after I’m back to work.

But I was saying…how can I nicely download the email as a real txt file? If you right click on a message, the contextual menu that appears is showing you a “Save as” option. If you continue, your message is saved as an eml file. An eml file is a nice thing to store, you can import it and read it with another email clients, and it comes with meta information. But it’s not nice to read. As it is said nowadays, it’s not human-readable. This is not exactly true, since if you do more over the downloaded file, you can somehow read it. And if you can read it, you can mine it.

So I went for an add-on. Ideally, I wanted an entry on the contextual menu offering me to download the whole folder as a text file, but I didn’t find it. I was fiddling around with several add-ons, but my solution was, at the end, ImportExportTools. With this add-on, you get even the option of downloading your email as PDF!

The procedure to install it is quite easy, but not standard. You download the add-on here, and then install it with the Add-on manager. Go to Menu –> Tools–> Add-ons, and look for the Extension section to the left. Since it’s raining heavily outside, I even did a screenshot for you:

adds-on You see? Peanuts. Click on the wheel, and choose Install Add-on From File. Navigate to the place you downloaded ImportExportTools*.xpi and restart Thunderbird. Now, when you right-click on a message, after Save As, there is a new option called Save selected messages, that opens up a new menu with all the options you may need. The rest is up to your imagination. Or I could say, my imagination 😛

Have a nice holidays and enjoy your weather while you can 😀

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Geography issues

It is hard to understand the geography of this new world. In principle, one can think it’s not so different, since people tend to stay around the area of the City they end up after falling, the inhabited clusters we call kernels. The most striking physical difference is, if we ignore the green moon with the tail and the space time inconsistency, the lack of our oceans. Despite of it, water seems to flow through a more extensive, world-wide and heavily packed, network of channels that we call in general the Rivers, and locally, only the river.

Some rivers seems to flow even against logic, upstream. Some of them are too straight to be natural, but the majority of them go through the path our rivers flow. So they are dubbed as the Earth ones, Thamesis, Donau, Ebro, Amazonas, and so on. Since we don’t have a reliable map of this earth, we can’t say all the Earth rivers are here, either that they follow the same route. Some people tried already to estimate the total amount of water, based on the number of rivers, the water speed, and so on. As far as I understood, our water is there, meaning this is still a Blue Planet, but it is distributed more evenly, instead of on big seas. There are small lakes, for example on the empty Mediterranean there is an agreement to call the water surface remaining close to Greece Thalassa,  Jadran to the equivalent Adriatic, Tyrren to the one around Corsica, and so on. I don’t know the names of the other lakes, but they exist all around. Then you have the oceanic trenches. The Mariana trench, Puerto Rico, and Cabo Verde were reported to be full with water, but some other trenches were missing. There were also new ones, like the Mid Atlantic one.

The other mystery (or not so mysterious if you think about it) is where are our trees, where are the forests. This dimension seems to be sun scorched earth, the yellow being the predominant color. The obvious answer seems to be on the Moon. The moon here is the green lung that on Earth is the Amazon, or the plankton of the seas. The accepted theory is that there is a flow of CO2 to the moon, and a flow of O2 back, through the green umbilical cord the transporters are using. Or something like that.

But to have an explanation to the problem of how we’re able to breath here is not meaning we understand it all. And the biggest question of all, the question that is our subject of research, is still unanswered. Who built the City and why?

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Not so easy

Sorry guys but it looks like I can’t comfortably connect from here, so probably this blog will experience a holiday break. Besides, I’m in another time zone, which adds a plus to it if you are a man of costumes. Please keep in touch!

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Kernel Seville

Right after we finished our onigiris the mecacar slowed down. From before, I know that a decrease of speed means the destination is close by or a change of path. Sometimes, you simply look like going in a straight direction, but in reality what you follow is a curve, and sometimes, these curves get extremely sharp, to the point that you can feel the centripetal force somehow drawing you to your left or to your right, like in an adult version of a merry-go-round.

I remember the Seville from Earth, of course. The area we are approaching has been populated mostly with the migrants from the original one. Amongst them of course you had the city lovers, those that were able to kill somebody for saying that they didn’t like their town. It’s true that Sevilla, the original one, not this kernel version, is a truly gorgeous architectonic pleasure, with the biggest gothic cathedral in the world in the very heart of the city. Oddly enough, kernel Seville has some kind of temple in the center also. Unfortunately for the deeply catholic lost inhabitants of the original one, it is not as gorgeous as the original. The style, that I studied already, is interesting enough: as other big temples of the Yellow Earth, it’s a multipurpose space, but this one, as a difference with the others, has a central high altar dedicated to the Sun. That one, of course, was the one brought down by the migrants fallen from Seville to build up its new Cathedral.

Actually, the image they now walk through the kernel in processions, from time to time, is not exent of some oddworld beauty. The tradition of parading our Lady of the Sun, a vaguely feminine figure dressed with gorgeous mantles from the original Seville, has now, as far as I know, 50 years of history and a loyal and growing group of devout followers. To the point that, despite of the ancient roman styled architecture predominant on this kernel, one could feel kernel Seville is simply a neighborhood of the Sevilla from Earth. I heard they’re even going to start their own Feria!

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