Closed for Chrismas

I’m afraid with all the hassle of Christmas dinners, outings, and playing with the new toys that we all got, I don’t have time to update this thing as I’d like to. In the meantime, if you happen to pass by, merry christmas and a happy new year! And as they say in the place we live

Frohe Festtage und einen guten Rutsch!

If you are bored, maybe you can start reading my blog from the very first “alien” post, and send me your comments about coherence and character development. I need to make sense out of all of it, peel the dead parts, edit, and clean. Probably I will not finish it before I come back to my daily working routine (and daily posts) but I need to do it, at one point. It needs to be done, before it’s too late.

I read you around. If possible.

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The Plan

– So, knowing what you know, what do you suggest we do? – I venture to ask.

– Well, it’s hard to say. – He does the pause that means that he’s no doubt calculating the probabilities, or probing the future. Using his prospective sense. – I’m really upset with you guys. But I could say, it was not your fault, it’s the society you brought with. Seriously speaking, I’m with the revolution, so to say. Burn it all and start again from the ashes! – He laughs loud. I know he’s joking, otherwise, it’s kind of scary.- Let’s be rational. We could, so to say, find a way out. I will start by probing the collective mood. If the conditions are right, little by little, with the help of people like you, in a couple of centuries we can be the most egalitarian society since the greeks…and they had slaves.

– I don’t have two hundred years. – I get the clothes he’s handing me. They of course fit me, since probably they are just printed. I smell the t-shirt. Yes, just printed. The design, not that I care about it, is no doubt a free one. No time to choose, I guess.

– I know. But that’s the best way to go. That’s the way we’ll take. – I throw him an empty can, that hits him in his back. – Auch! I see. Yes. Now, what do we do to achieve that future, while keeping you alive? – I take the camouflage belt. Oddly enough, it does not look like an electronic component. A bird is telling me that the belt is a fake, but I ignore it…I will test it as soon as I can. – You need to  find out the connection between your boss and the people that support him, and the assassinations. You don’t need the reason, jut the connection. After that, I suggest you go to the press, tell the whole story, and get the glory. That’s it. Pretty simple, isn’t it? People will no doubt about it believe you over all, since you’re a Cop, aren’t you?

 

Awake (II)

Despite of the good amout of chemistry amongst us, I was not yet convinced. Anyway, what are my options? I could, I guess, play the good friend until finding out a way to escape, then run away. But run away to where? My boss was probably involved. And the size of it was so big that there was nowhere in the planet I could hide. They could track me, program the cameras to react to any pattern similar to my body shape. That was an ancient technique, proven to work efficiently, if given the right amount of time. It has happened before. I could even remember some examples from my training, how the position of the subject was narrowed to the square meter, then trapped. Of course, you need to program the cameras to do that, leaving all the other tasks aside. But we can afford it, we have the Pioneers looking for the health of our environment, haven’t we?

Could it be possible to interfere with the cameras? I mean, is it possible to have some kind of electronic cloaking device that makes them turn away their lenses? I’m sure it is. And how do I get it?

– Once more, I know what you’re thinking. – My friend interrupts my line of thoughts. – You traditionals are sometimes so predictable. – I will not take that as an offense, after his speech. – You think they will follow you here, and you want to avoid the cameras. Am I right?

– Yes. – I take the opportunity to stand up. My legs are still able to support my weight. My forearm is hot. I look at it, but the bullet wound of course is covered by bandages.

– Then I have the right solution for you. Or I could say solutions. – He goes to the closest table, and takes something that looks like a belt. Then I find out I’m naked. My body is covered with bruises. – This is a black-market item. I don’t know who developed it, but it’s not new. I bought it from a friend of a friend, because I wanted to feel lonely, so to say, for a while. That’s the advantage of being a second-class citizen, that people don’t ask you so many questions, they simply assume you want it for some illegal thing. By the way, in case you ask yourself about it, yes, I tried it, and yes, it worked. You can stand in front of a camera, even take it with your hands, that there will be no record of you. How the magic is done, I can only guess, but my favourite is that the belt access to the RAM of the camera, and send a signal to impose a previous image without you on real time. Or maybe it simply cuts you out. Photoshopped, that the said in the XX century.

Awake

– Feeling better? – I do.- Your wound is almost healed. You passed away after we found out you were not dead…but that’s OK. – I smile. My friend smiles also. I still didn’t figure out if he’s one of the good or the bad guys. I suppose I need to postpone the issue. He hands me a silver ball. – Do you want to connect? I know your interfaces are fried, but we have something better. We call it “the magic ball”: it reads your thoughts and translate you to the network. – I blink, to express my surprise. I didn’t try to speak yet. – Yes, you know so little about us…but I think now all of that doesn’t matter anymore. Or it will not matter, right?

– What the hell are you speaking about? – I manage to shout. My voice sounds rough, but appart from that, everything looks fine.

– Calm down, man. Now I think it’s safe to share a drink. – He offers me a can. I take it, and temptatively I sip it. My throat takes the liquid like a desert takes the water, but I stop after a sip.

– What do you know, and how did you find out?

–  Do you know you mumble when you sleep? – I didn’t. – Yes, it was very entertaining to hear you while you were unconscious.  All these things about the killings, and us in the center of some kind of conspiracy against your government…why didn’t you tell me before? – I drink the half of the can before answering. He doesn’t look angry or something.

– I didn’t trust you. You know, we are friends, but that doesn’t mean we need to share a common view of the future of the mankind. – He laughs, in the way he does when he’s pleased about something. – In my concern, we are both humans, but I can’t say you think the same.

– Why shouldn’t I? – He quickly replies. – Before we went to Space, people were already labeling humans. Black, white, asian…Because those were, as later demonstrated by the genetic science, just that, labels. As arbitrary as dividing them by eye or hair color, or ability to understand math.

– But you do have more abilities than us, don’t you?

– And why if we have? Does it matter? The important thing is that we are brothers, we come from the same gene pool, and we can communicate with each other using a common language. That is more than the people of the XX century were able to say. Our abilities, as you call them, are like the ability to appreciate or create art or math: some people have it, some people not, but you can develope them in the right environment. In a thousand years, we will be as different as the Asian and the Caucasians of the XX century. A point of view, only. A point of view. – He repeats, with a funny tone. I wonder if he’s quoting somebody. Looking to the ceiling, he finishes his drink, and smashes the can in the way I saw him doing before, when we were going out together. – So will you trust me, or not?

– I will.

– Then let’s fix this together.

 

Dynamo module for CentOS 7

 Dynamo is a software environment for subtomogram averaging of cryo-EM data. That is quoted from its wiki.  The standard dynamo installation procedure you can find here. Actually, it is working out of the box: you download the tarball, untar it on a specific folder, source the right script, and it works! Supposing I install it on /usr/local/, something like

source /path/dynamo_activate_linux_shipped_MCR.sh

will allow you to get the dynamo GUI if you type dynamo X afterwards. Note that as quoted, starting the Dynamo console can take some time. This is the standard output you see if everything is right:

dynamo X
Initializing MATLAB Runtime version 9.1
"MCR libraries starting dynamo.
Starting the Dynamo console can take some time. 
A good choice of MCR_CACHE_ROOT might speed this up."
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Warning: MCR_CACHE_ROOT is empty.
 Initialize this variable in your shell for a quicker startup.
 To know more, type:
 dwiki MCR_CACHE_ROOT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Warning: MCR_CACHE_ROOT points to non-existing location: 
 Correct this variable in your shell for a quicker startup.
 To know more, type:
 dwiki MCR_CACHE_ROOT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Launching a Dynamo graphics terminal in a separate window....
.... done

So how do we “modulate” this thing? First, as suggested, I recompile the graphical libraries. Here you find how to do it for Dynamo. Our output looks like this:

 ## > source config.sh 
----------------------------------------------------------------
 
 Configuring makefile for the CUDA installation in your system
 
Looking for a CUDA installation in this environment:
 Found CUDA nvcc compiler at /usr/local/cuda-7.5/bin/nvcc
 CUDA installation assumed to be in /usr/local/cuda-7.5
we will use /lib64 (standard procedure)
 
Substituting the CUDA location assignment:
 CUDA_ROOT=/usr/local/cuda-7.5
with the actual value:
 CUDA_ROOT=/usr/local/cuda-7.5
 
 [ok] 
 
 you can now compile the CUDA utilities by :
 make all 
 or :
 make motors
 if "make all" produces an error when 
trying to compile the Nvidia utility infoGPU
 
--------------------------------------------------
## > make clean
rm bin/* || echo "No previous CUDA 
executables found in /cuda/bin" 
## > make all
/usr/local/cuda-7.5/bin/nvcc -o 
bin/dynamo_compute_iteration_spp src/
dynamo_compute_iteration_spp.cu 
-lcudart -lcufft -lcublas 
-L/usr/local/cuda-7.5/lib64 
-I/usr/local/cuda-7.5/include -Isrc -w
echo 'Compilation of Dynamo completed. 
Use make extended to include Nvidia GPU'
Compilation of Dynamo completed. 
Use make extended to include Nvidia GPU

I will skip the “make extended” on this installation. It’s time to write the module. My first idea is to source the script on the module definition. Unfortunately, this has mixed effects: some variables seem to be correct, but others not. I blame the mix of languages of the issue, and I try to set up all the variables we have when we source the script “dynamo activate” for the TCL module. The result looks like:

#%Module1.0###################################
##
## modules dynamo/dynamo-1.1.226
##
## modulefiles/dynamor/dynamo-1.1.226 dynamo 1.1.226 module
##
proc ModulesHelp { } {
 global version modroot
puts stderr "dynamor/dynamo-1.1.226 
- sets the Environment for using dynamo 1.1.226"
}

module-whatis "Sets the environment for using dynamo 1.1.226 "

# for Tcl script use only
set topdir /usr/local/dynamo-1.1.226
set version 1.1.22
set sys linux86

prepend-path PATH $topdir/

# additional env variables 
setenv DYNAMO_FOLDER /usr/local/dynamo-1.1.226
setenv DYNAMO_ROOT /usr/local/dynamo-1.1.226
# Location in the distribution expected to have an MCR
setenv MCR_ROOT $topdir/MCRLinux

prepend-path PATH /usr/lib64/qt-3.3/bin:/usr/local/bin:
/usr/bin:/usr/local/
sbin:/usr/sbin:$topdir/matlab/bin/:
$topdir/matlab/src:$topdir/cuda/bin:
$topdir/mpi:$topdir/examples:$topdir/doc

prepend-path LD_LIBRARY_PATH $topdir/MCRLinux/runtime/glnxa64/:
$topdir/MCRLinux/bin/glnxa64:$topdir/
MCRLinux/sys/os/glnxa64:

I decided not to display any message when loading the module. It took me some time to tune the libraries, but after doing so, everything looks fine. This is what I get when I run a test project:

./testproject.exe 
Initializing MATLAB Runtime version 9.1
"MCR libraries starting dynamo_execute_project. 
Opening MCR to launch project."
-----------------------------------------------------
 
Project: testproject
 contains 3 rounds, totalling 3 iterations 
 will run on destination "standalone_gpu" on 1 cores
 
------------------------------------------------------
 
Your project invokes multicore operations (2 cores required).
Dynamo will now test your hardware to check that 
it can run the project.
Alignment step: 1 cores, Averaging step: 2 cores
Starting parallel pool (parpool) using the 'local' profile 
... connected to 6 workers.
[mbparse.multicore.checkPool] Closing previous pool. 
You asked for 2, pool contains MORE (6)
Parallel pool using the 'local' profile is shutting down.
[mbparse.multicore.checkPool] 
... previous pool of 6 workers closed.
Starting parallel pool (parpool) using the 'local' profile 
... connected to 2 workers.
[mbparse.multicore.checkPool] Opened pool for 2 workers
 
- - - - - - - - - - - - - - - 
- - - - - - - - - - - - - - - 
[gpu check] Checking the GPUs
[gpu check] Requested devices: [0]
- - - - - - - - - - - - - - - - 
-------------------------------------------------------
Iteration 1 corresponding to round 1
Starting iteration at 15-Dec-2016 12:58:57
[setup] Parameter set is in 
./testproject/cards/ite_0001/card_ite_ite_0001.card
************************************************
********** NEW ITERATION ***************
********** iteration: 1 
************************************************

... bla bla bla...
[Check]: dynamo_iteration_check
('./testproject/cards/ite_0003/card_ite_ite_0003.card')
 Starting time: 15-Dec-2016 12:59:20
iteration 3 ok

So it runs. Time to distribute the module, and hear the complains from the users 😉

Options

I want to speak about it. Supposing I can, right now, I don’t know what to tell him. He knew the trouble I was in. He knew my theories about. Shall I assume that he’s not, in any form, connected with my attack? And more important, can I rule out that he’s not trying to find out how much of the plan I know?

I could use additional computing power at this moment. But my private network is off since that encounter. I should have set up some alarms, but I didn’t: people don’t go around killing other people’s electronics. I need, therefore, to rely once more on my memory.

Let’s start gentle. The Pioneers are not mixing up with us, except in certain areas. This means, in principle, they don’t want to. They have access to our city in a way we will never do. That will mean the chances they found out what is going on are bigger than for us, the “traditional” humans. If I want to make a leap of faith here, I will say they don’t care about it, in general. They are beyond the good and evil here. But does it mean they help them, or not? Does it mean my friend is aware of the plot?

I need to assume they are as human as we are. Corruptible, with independent thoughts. Therefore it is possible a small fraction of the Pioneers is actively supporting the plan. It is possible they have something they want, like a new, more friendly, colonizing target. Worst case scenario, from the small sample I have, I will say 50% of the Pioneers are in. All of them I met while going out were friendly, but I can’t discard that was a misinterpretation from my side. I can be very bad reading faces. On the other hand, most of the “traditionals” I met in random events (like in that official dinner half a year ago) do not consider the Pioneers as a part of our society. I could say 90%. Ignorance is a good seed for hate, and we definitely ignore what they are, that is, the guardians of our biosphere.

Where does this lead us, where do we end up? If I trust my guts, I need to tell my friend, as soon as possible, what is going on, and get him on my side, as soon as possible, as much as possible. If only I were not so dizzy…

A good friend

First thing I see after opening my eyes is my Pioneer friend. He’s looking at me, waiting for me to tell something. I don’t.

– Feel better now? – I blink. I’m actually scared to speak. – I guess that’s a yes. – I try to look around, without so much success. My forearm feels numb. So everything was true: the chasing, the fall…I try to speak.

– How long…- My voice sounds broken.

– How long? Does it matter? The important thing is that we recovered you alive! Do you want to hear the story? Actually, it’s kind of funny. Just nod if you want. – I nod.- You know we “the Pioneers” are in charge of the maintenance of the life support, in general. -I nod again. – Alright. What you don’t know is the degree of commitment it means to endure such a general job definition. – I nod, since I don’t want to make him think I’m vanishing again, or losing interest. – Basically, all of us, and I mean all, are able to sense small variations on the environment conditions. That was considered, at the moment of our rise, an evolutionary advantage. Imagine that you land on a strange planet, like this one, and you are immediately able to say if you can breath the air safely, or if the water is good. Yes, I know. Who will land on an unknown planet without a previou analysis? But I must say to have such an ability has another use, more daily. For example, I’m able to smell how good is a whiskey, or if  the food you’re offering me is poisoned. It can become quite handy sometimes. – He smiles. – Right. The story. So here I am, enjoying my free time when I get the call from a friend. Yes, I have other friends. We can speak about it when you’re OK. So this friend , that happen to be in charge of the water supply, tells me that he tastes something funny on the water coming from the North Small Chamber, one of the subterranean reservoirs that provides us all. One part per million, he says, is contaminated with some organic substance that may have human origin.

The North Small chamber is, your lucky bastard, one of a few accessible by train. We do go there to check the heaters that melt the ice, from time to time. But I’m going sideways. The thing is, I decided myself to investigate personally. We rely a lot on our famous ESP, you know, that is called, in case you want to call it properly, quick and random analysis of variables. – He makes a break, to drink something. A beer, looks like. I wonder if his sense of poison is also working to clean it up, if needed. –  I like to call it ESP, it makes me feel like I’m a superhero or something. So this ESP tells me that I need to go to investigate the North Small Chamber. Since, as you know, most of the time we only are around to create problems, I decide to follow my hunch and take a train to North Small.

The ride is a few hours. I mean, if the ESP is beeping you, you better obey, independently of how annoying the task you need to do is. In my case, it was meaning organizing a search team, just in case the organic substance happen to be something more important than a dead minipig, or some other animal of that type. – I apparently made some kind of face, since he stops to look at me. – Yes, it happens. We have a very active biosphere, here. What do you expect life to do, to behave when you say don’t go this way? We have some outliers in the tunnels. Some of them even went feral. – He sips his beer. – Once more, sorry I go sideways. Your story. Guess what? You were the minipig this time!

I thought you were dead, since we found you floating, actually quite close to the ice heaters, that probably helped to keep you alive. Surrounding you, there was a pool of blood, slowly mixing with the water. I fished you out, and, no more question asked, I brought you here. To our labs. – I try again to move my head, but I fail. – So if you could be so kind to answer my question, I’ll be glad… – I smile, and have a look to his beer. – That’s not the question. You’re not yet ready to drink. Besides, you will not appreciate it, you’re now heavily drugged. The question is: how the hell did you end up floating on North Small, with a bullet in your arm?