Install EM Hole Finder on CentOS 7

I spoke about the leginon/appion pair. You have leginon for automatic EM data acquisition, and appion for processing. They are super-big complicated software packages, designed to work under CentOS.6. Unfortunately, we are very modern, and we use CentOS.7, so, it’s time to have fun upgrading something that is not mine!

I will follow the original installation guide as described on the Appion page. Even I will use the same paths.  I will quote the steps, and comment them as they fail.

yum install git python-virtualenv libjpeg-devel -y  --> OK
 easy_install pip  --> OK
 cd /opt  --> OK, of course
 git clone https://github.com/hbradlow/em_hole_finder  --> OK
 ls --> OK, of course
 cd em_hole_finder --> OK, of course
 virtualenv env 
New python executable in env/bin/python
Installing Setuptools....................done
Installing Pip............................done.

–> OK, now we have (env) on the prompt. I continue.

source env/bin/activate  --> OK
 pip install numpy  

Downloading/unpacking numpy
 Downloading numpy-1.11.2.tar.gz (4.2MB): 4.2MB downloaded
 Running setup.py egg_info for package numpy
 Running from numpy source directory.

 blas_opt_info:
 blas_mkl_info:
 libraries mkl_rt not found in

.. it goes no for a while, but at the end
Successfully installed numpy
Cleaning up...

–> OK, then , despite of the NOT AVAILABLE messages. I will ignore them later on also.

 pip install Cython
Downloading/unpacking Cython
 Downloading Cython-0.25.1.tar.gz (1.7MB): 1.7MB downloaded
 Running setup.py egg_info for package Cython
 Unable to find pgen, not compiling formal grammar. 
 warning: no files found matching '*.pyx' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.pxd' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.h' 
under directory 'Cython/Debugger/Tests'
 warning: no files found matching '*.pxd' 
under directory 'Cython/Utility'
Installing collected packages: Cython
 Running setup.py install for Cython
 Unable to find pgen, not compiling formal grammar.

.. it goes on for a while, but at the end

Successfully installed Cython
Cleaning up...

–> OK. Next one

pip install PIL
Downloading/unpacking PIL
 Could not find any downloads that satisfy the requirement PIL
Cleaning up...
No distributions at all found for PIL
Storing complete log in /root/.pip/pip.log

Similar trials fail to find the package also.

pip install PIL --allow-external PIL --allow-unverified PIL

So it looks like there is no PIL for us. Google is recommending to install  pillow instead.

pip install pillow
Downloading/unpacking pillow
 Downloading Pillow-3.4.2.tar.gz (10.8MB): 10.8MB downloaded
 Running setup.py egg_info for package pillow
.. compilation goes here for a while ...
----------------------
 PIL SETUP SUMMARY
 --------------------
 version Pillow 3.4.2
 platform linux2 2.7.5 (default, Sep 15 2016, 22:37:39)
 [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
 ------------------
 --- JPEG support available
 *** OPENJPEG (JPEG2000) support not available
 --- ZLIB (PNG/ZIP) support available
 *** LIBIMAGEQUANT support not available
 *** LIBTIFF support not available
 --- FREETYPE2 support available
 *** LITTLECMS2 support not available
 *** WEBP support not available
 *** WEBPMUX support not available
 ---------
 To add a missing option, make sure you have the required
 library and headers.

–> OK, we go ahead

 pip install scipy
Downloading/unpacking scipy
 Downloading scipy-0.18.1.tar.gz (13.1MB): 13.1MB downloaded
 Running setup.py egg_info for package scipy

.. also we get the NOT AVAILABLE message for openblas_lapack_info
Cleaning up...
Command ... 
failed with error code 1 in /opt/em_hole_finder/env/build/scipy

–> maybe NOK, but we go ahead. The error seems to be on installing some headers for the local python. Just in case I try to install scipy with yum

yum install openblas lapack gcc-gfortran python-scipy

–> also NOK, but we go ahead

pip install scikit-image
 Downloading/unpacking scikit-image
 Downloading scikit-image-0.12.3.tar.gz (20.7MB): 20.7MB downloaded

.. a lot of dependent packages are downloaded and installed..
Cleaning up...

Command ... 
failed with error code 1 in /opt/em_hole_finder/env/build/scipy

–> also NOK, but we go ahead, as before

pip install ipython
Successfully installed ipython setuptools 
decorator pickleshare simplegeneric traitlets 
prompt-toolkit pygments pexpect ipython-genutils 
six wcwidth ptyprocess
Cleaning up...

–> OK, we go ahead

pip install wsgiref
Requirement already satisfied (use --upgrade to upgrade): 
wsgiref in /usr/lib64/python2.7
Cleaning up..

–> So OK.

The rest goes smoothly. Once added to the module, the initial tests look fine despite of the errors with the headers. To fix that, we move out of our (env) and try to install them with the “default” python.  Scypy I have already. I can test it opening a pyton prompt and typing “import scipy”.

pip install cython
...
Successfully installed cython-0.25.1
pip install scikit-image
...
Collecting scikit-image
 Using cached scikit-image-0.12.3.tar.gz
...
Successfully installed cycler-0.10.0 dask-0.12.0 matplotlib-1.5.3 
networkx-1.11 pyparsing-2.1.10 python-dateutil-2.6.0 
pytz-2016.7 scikit-image-0.12.3 toolz-0.8.0

–> So OK. Now to wait the output from the users.

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After party

I remember that now because it can be important.

– So you decided to contact me, after all. –

That was his first phrase when we met the next day. It sounded mysterious, and sincere. My new Pioneer friend had, as he explained me, several times before met people that were calling him friend one night, fiend the next. So he was gladly surprised I was not one of them. On my side, I must say I was hesitating to contact him after the first night of fun. My fear at that moment was of being misinterpreted as a gay, or something on that line. I knew he liked girls, but I was not sure he got my preferences. Don’t misunderstand me, my parents were gay, and I have nothing whatsoever again that sexual option. But I tend to like girls more. I guess everybody needs to take a side.

The place we met it’s irrelevant. I agreed on a popular area on that days, plenty of pubs, but safe enough, on Babylonia. I did know at that moment the existence of the LowLands, but as a newbie student, I was not brave enough to explore it. But let’s go to the facts I learned that day.

One: Pioneers are having longer lives than us. I don’t know how much longer, but longer.

Two: they call us traditionals. And they consider themselves the current humans. They somehow think that we are a branch of the mankind that resisted to evolve to a more practical level, more adapted to the interstellar media. I’m not going to discuss that now.

Three: they don’t have implants, neither personal networks. But they do interact with our networks. How they do that, I can only speculate. My guess is that they have at home nice body scanners, or a haptic surface, or something on that line. But nothing attached, nothing movable as we have. As far as I remember from the history books, people in the past were even interacting with the network using physical keyboards only. I could realize that, I think, and he didn’t speak to me through a keyboard when we fixed the appointment. These kind of things can be quickly pinpointed. I think.

Four: they don’t have jobs, as we do. Everybody knows how to do everything. They call it the multitasking advantage. So they do this or that, as requested: fix a pipe, dig a hole, build a park. They are very good on those things, building habitats. How they learn that, I have no idea. Maybe they use the same mysterious haptic space they use to interact with our networks. I do think they are not greedy, and you will not find them living on the Village, for example. Therefore they can live with the default salaries, or maybe, get the missing credits by doing some maintenance job, or borrow them from other pioneers if needed.

Five: they don’t have government, but they do recognize ours. And I can almost assure you that this is not exactly true, because from later conversations I found out that they meet from time to time to discuss things. How big are this meetings, or who’s going to them, remains a mystery also. Maybe I should ask my boss about that. Or even better, I will directly ask him about it.

What the hell, maybe I should ask him to help me to solve the crimes.

 

Windows XP CSC bloating

I have an XP computer connected to a device. The XP computer allows AD login. It has a reasonable hard disk size for an XP computer, 320 GB, but each 3 months people get annoyed because the hard disks appear to be full. So they call me.

I didn’t configure the computer. But I know the device connected to it is not producing enough log files to fill 250 gB in 3 months. So why is the HD full from time to time? This time I decided to take it with me to the office (leaving the precious device off) and check in detail. The answer was easier than I expected, but cryptic: the enabled file cache when working offline is producing CSC files. You can find out in this link everything you need to know about the Windows CSC folder. There are plenty of answers to the question why is the Windows folder too large on the web. But you need to know about the issue exist on the first place.

So what to do to avoid that to happen?  Disable the offline files. It turned out that this operation is as quick as setting up an folder option. I will, anyway, never get the answer to the question why it was set up like that in the first place. I placed it like that on the lab, and all is calmed up to now. Next battle: upgrade the computer (and the 3000 euro software it carries) to Windows.7 😦

Questions

– What are you going to do with her? She’s not dead, right?

– Also not alive, my dear colleague. – I’m pretty sure my sensei is being ironic there.- If we refer to the books, “any entity able to think, express his, her or its opinion in any way, and interact beyond the Turing thresholds will be considered alive by the law, and treated as alive under all effects”. I don’t think she’s able to express any opinion anymore.

– But we don’t know if she’s able to think.

– Good point. – He seems to hesitate.- Well, we have her cyberspace. We should perform an autopsy over her personal network. Maybe there is residual activity, somewhere. Maybe even she managed to save a running copy of her memories, somewhere. Maybe it’s very interesting to have a look to what she recorded. If she recorded something. Also, we need to check her contacts. – He smiles at me. I feel a warm wave of reassurance. I’m not as bad Cop as I think. We stare at each other’s eyes for more than a minute, ignoring the body close by. His eyes are completely dark, I can’t appreciate any movement on his pupils. They are so dark they look dead. My warm wave is gone. Now I’m concerned. Then he speaks.- Can you take it from here?

– Of course I can.-  There was no other answer possible. He then crosses his hands in his back, looks down, adjusts his sandals, and heads in the direction of the door.

– So when do you expect to have some results for me? – He suddenly turns and look at me. His eyes are so sharp that I feel like being impaled by cold icy black nails. – You know, some people are starting to realize that the investigation is not going as fast as it should. Do you need some help? I gave you already a weapon, do you want something else?

– No, I’m fine.- I don’t know what to ask for. A mate? A personal camera? A cloaking device?  He seems to change his mind and with parsimonious steps comes closer to me. I’m petrified.

– There is no dishonor on asking for help if you need it. – For some reason, he is now whispering to my ear. His head is 5 centimeters away. I smell a faint curious scent, that reminds me when we were together at the onsen, when everything started. Like a mixture of bamboo and wet hair. – This is a very complicated issue. And we don’t want to loose control over it. Do you understand? – I nod, slowly. He retreats. The smell is gone. – Well, well. Then, I definitely don’t have any more business here. We have faith in your capabilities. Your scores are the best. You will solve it at one point. But I can help you with the number crunching. I’m your colleague, and your problems are my problems. – He’s abandoning the room. I see only a part of his back, when he shouts back. – Contact me as soon as you have some news ! – And he’s gone.

 

Class of ’98

We were 20 in my class. You may think it’s a lot of people, but it was not. It turned out that out of these 20, at the end, only one, me, managed to join the Corps. I could say, anyway, that I expected that. When you study something at the University, you do it not expecting to work on it. The University was built as a kind of temple of knowledge, in the same way the Temple is for the people with religious needs. So you don’t expect anything in return. Your life can’t be based on it. We were a bunch of dickheads, all of us, just looking for a new life goal by digging our life rules out of the crap of our civilization. For example: do not modify digital records, unless owning them or having permission from the government. This meaning that, all that awful parties at the campus, all those annoying flirting deceptions, were recorded by default, unless specifically deleted by one of the Corps. That is what we learned then, and what I know now is that these recordings are kept only for three months, unless keeping them is strictly requested by a legal tutor, owner or authority. Meaning all these gorgeous parties, at the end, against our wishes, were deleted. We were partying at that moment like beasts, like there was no future.

For example, my first encounter with my best friend was in a party. There is no official recording now, but I remember it was a good one. We started at the University, celebrating the birthday of somebody of my class (I don’t remember his name, and I don’t want to remember it) and after ending up with everything that was drinkable on the room, we took a tube to the Low Lands. Somebody (again I don’t remember the name, but I could identify him if I see him) somehow prepared a hall for a live concert and an afterwards party. The place was in the middle of a hot area. The cameras came with us, since we were an government investment, but that didn’t stop us. There was the live music. And the life sex, by spontaneous performers. The doors to the hall were open. Everybody was invited, provided they knew there were cameras. The point is, the cameras don’t record everything everywhere, so sometimes it doesn’t matter if you have cameras or not.

He was speaking with a girl of my class. The lights were, again, not allowing me to identify him as a Pioneer, but I never cared. The thing is, I previously tried to approach to that girl, but she kicked my butt when I was thinking I was going to have a chance, so I was curious about the type of man she liked. It turned out, for my luck, that she kicked out my future friend also. And he ended up close to me.

– A real bitch, isn’t her? – He told me after he landed by my side, before finishing his drink, and immediately refilling it, not without offering me one too.

I said something defending her. He looked at me, I remember, like reading my mind. Then I realized what he was, but I decided to ignore it. He asked me about her taste in sex. I asked him about his taste in girls. We laughed, spontaneously, together, like old friends. We shared some common failures. It turned out we shared some common preferences, also. Then we walked around, looking for targets, in the hope that one plus one was more than two. The party was really good, but not for us. We drunk a lot. We spoke a lot. That day,  I think, we connected.

Bad news

– Thank you for coming so fast. – My boss requested my presence, and in the current situation I had no excuse but to come. – We have here another body. I didn’t want to tell you through the network, just in case the news are intercepted.

I got the message from him right before I was ready to start again with my list. It was short and clear: we need you here. I was requested to go to another location in my neighborhood. I didn’t know what to expect. But I didn’t have the mood to investigate the media before arriving. The place happened to be a standard, middle class, one-store-five-rooms apartment. The profile of an inhabitant of these kind of flats are educated people, with a more-or-less healthy bank account. Like myself. No squatters, neither Pioneers, nor social workers. Also, not a banker. Bankers are more likely to live in the Village.

– As you see, there’s nothing unusual here. – There was a woman laying on the sofa. Over the table close by, a lot of paper magazines, an empty bottle of whiskey, a couple of crystal objects and some dirty dishes. On the corner, close to the kitchen, was exposed a red and shiny last-model multi purpose 3D printer that I could never buy with my salary. The kitchen table was clean, whatever that meant. The appartment was exuding class but not money. Let’s say it was classy but not pretentious. – She’s alive, if you ask me the question. – I was about to. – And that was a surprise. – My boss walked around, touching in a delicate way this object here, that floating screen over there. – We were called by her institution when she didn’t arrive in time, first time in cycles. – He took something looking like a very complicated glass of wine, smell it, and left it exactly in the same place. – They suspected something always. She has an history, you know. – I dont. – Once she managed to cook the brain of her boyfriend. – I smile. She’s beautiful, but I don’t know if enough to fight for her. – But you can read her historial later. I could even recommend to read it, since it’s quite interesting. – My boss walks around, like if the condo is his new domain. He goes to the kitchen table, touches it with his index, look at his index, and cleans it on his police kimono while making a disapproving face. – So the facts. In the last 500 cycles, she never arrived later than expected. She was a model worker, never late, never angry. But you need more than punctuality and efficiency to clean your history, so she was being watcher. We had a camera permanently over her on the public areas. But today, even two hours after the time her office opens, she was missing, and not detected by cameras closeby. So they called us.

– Nothing unusual there, also – I ventured to say. I went closer to her and took her pulse. The heart was beating. Her eyes were blinking. Apart from that, she was a toy.

– The unusual thing is her state. It looks like all her nervous system is gone. – The eyes of my boss are on fire. I think he enjoys it, despite of his age. – Not only the spinal cord, or the brain, but all of it. Wiped out. Under all effects, this is no more smart tissue. – I poke her. – Your ugly carpet probably has more connections than this body.

– How this thing happened? – I don’t expect an answer, otherwise I’m not called to come.

– We don’t know. The cameras, as before, didn’t find out anything irregular. – He takes the decorated glass wine again. –  But it can be done, of course. You just need the right technology. And if somebody thought about it, it’s possible to buy it. The million credit questions are: who wanted her dead so badly that he or she poisoned her? and more important, why?

Dilemma

This is not going well. I don’t do it to reach a million readers, but I need a few to continue writing in a daily basis. That was why my other blogs died. Alright, I’m not being fair, livejournal died, and B2B was not maintained alone, so I don’t feel 100% guilty of that one. The only one that is still going well seems to be sociedadtecnologica. It’s a multiple-partnership enterprise, it’s in Spanish, and I’m not even a frequent collaborator. So I don’t know if it counts. Long story short, and I know I contradict myself when previously said that I’m going to post more varied things, but I may reduce the frequency of my posts. After all, I started this as a personal bitacora, not as a literary blog. Although it’s nice it can become, at one point, a literary blog. But more than a literary blog I think I will manage to get a literary graveyard of my previous publications. See you around.