Yo-Yo Ma & Andrew Bird
And music from the Appalachian Journey
Tinypliny's Journal
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10/21/2011 14:30 #55342
In love with...Category: music
10/21/2011 10:20 #55340
Learning to be a software carpenterCategory: goals
Coding is time consuming. I didn't really consciously think about this till my advisor asked me about the roadblocks to my progress in my dissertation. I thought back and it occurred to me that I was
Why am I doing this when I have a data manager for the data I am dealing with? Because it's insane to go whining to the manager the minute you want some data processing done. He has own Ph.D. to complete and has limited time and innumerable demands. So there is really no option but to power through all of this on my own. Besides, I think population sciences are *really* about statistics and data processing even though population scientists who don't do all this dirty work may persuade themselves that it is just about interpretation. It is as much about quality control in the data and seemingly trivial logical checks as it is about analyzing super-clean data in the end and figuring out what it could mean in the bigger picture of million other studies. I think it's important to acquire this skill so I can use it in my future. Not everyone has a data manager, a software coding bloke and a statistician to always help them.
The process itself is exhausting because it's like learning a completely new language without having ANY experience in how the semantics work. Apparently some people have observed this exhaustion and set up sites like "Software Carpentry":
It sets up a formalized framework within which you could learn these skills. I think courses like this should be mandatory to population sciences coursework. At some point, we need to realize that population sciences and bioinformatics are very similar in their scope and application. This is more true than ever as we progress rapidly towards HUGE datasets, complex data structures, multidimensional variables and the necessity of channeling all of this into interpretations simple enough to make sense to health-related and population policy-making.
- learning a somewhat new language (R)
- trying to code in it using concepts from statistics that I already have
- trying to generalize code so that it could be less repetitive and automate chores and processing
- trying to splice other languages such as latex and perl to interact with R code
- learning THOSE other languages
- trying to prevent errors in their interaction
- trying to write functions that would serve a purpose similar to "macros" on SAS but yet be understandable to me at a somewhat-novice level.
- debugging to see where it all goes wrong when errors turn up
- differentiating what is my code's fault, what can be changed in R preferences, and what is inherently the fault of the R build on the particular linux distro I am using.
Why am I doing this when I have a data manager for the data I am dealing with? Because it's insane to go whining to the manager the minute you want some data processing done. He has own Ph.D. to complete and has limited time and innumerable demands. So there is really no option but to power through all of this on my own. Besides, I think population sciences are *really* about statistics and data processing even though population scientists who don't do all this dirty work may persuade themselves that it is just about interpretation. It is as much about quality control in the data and seemingly trivial logical checks as it is about analyzing super-clean data in the end and figuring out what it could mean in the bigger picture of million other studies. I think it's important to acquire this skill so I can use it in my future. Not everyone has a data manager, a software coding bloke and a statistician to always help them.
The process itself is exhausting because it's like learning a completely new language without having ANY experience in how the semantics work. Apparently some people have observed this exhaustion and set up sites like "Software Carpentry":
It sets up a formalized framework within which you could learn these skills. I think courses like this should be mandatory to population sciences coursework. At some point, we need to realize that population sciences and bioinformatics are very similar in their scope and application. This is more true than ever as we progress rapidly towards HUGE datasets, complex data structures, multidimensional variables and the necessity of channeling all of this into interpretations simple enough to make sense to health-related and population policy-making.10/19/2011 19:20 #55335
Complete Fridge Wipe OutCategory: eating in
I am very close to a complete Fridge wipeout.
I currently have
- A wonderful big Cauliflower {needs to be used this weekend}
- 2 frozen bananas
- 1 ripe tomato {priority use this weekend}
- 1 orange
- 1/4th lb okra {super priority use maybe tomorrow}
- Ginger
- Garlic
- Some hot chillies
Well.. maybe not that close but still this is a reflection of workload. I think I might reach the wipout this weekend and give the fridge a scrubdown before I go grocery shopping.
I currently have
- A wonderful big Cauliflower {needs to be used this weekend}
- 2 frozen bananas
- 1 ripe tomato {priority use this weekend}
- 1 orange
- 1/4th lb okra {super priority use maybe tomorrow}
- Ginger
- Garlic
- Some hot chillies
Well.. maybe not that close but still this is a reflection of workload. I think I might reach the wipout this weekend and give the fridge a scrubdown before I go grocery shopping.
10/16/2011 20:39 #55323
Nvidia and Intel Graphics in Fedora 15Category: linux
There's something really wrong with my setup here:
Even though there is now a driver in use (installed from here: ) I still cannot adjust my resolution. I didn't install nVidia's own driver because of this article:
There is only ONE resolution in the display settings (1024X768). Attaching an external monitor results in the computer shutting down on its own. And there is no way to adjust brightness.
Aarrgh. Frustration ++. I am just going to ignore this today. I have too much work piled up.
01:00.0 VGA compatible controller [0300]: nVidia Corporation Device [10de:0df4] (rev a1) (prog-if 00 [VGA controller])
Subsystem: Toshiba America Info Systems Device [1179:fc31]
Flags: bus master, fast devsel, latency 0, IRQ 16
Memory at f6000000 (32-bit, non-prefetchable) [size=16M]
Memory at e0000000 (64-bit, prefetchable) [size=256M]
Memory at f0000000 (64-bit, prefetchable) [size=32M]
I/O ports at e000 [size=128]
Expansion ROM at f7000000 [disabled] [size=512K]
Capabilities: [60] Power Management version 3
Capabilities: [68] MSI: Enable- Count=1/1 Maskable- 64bit+
Capabilities: [78] Express Endpoint, MSI 00
Capabilities: [b4] Vendor Specific Information: Len=14
Capabilities: [100] Virtual Channel
Capabilities: [128] Power Budgeting
Capabilities: [600] Vendor Specific Information: ID=0001 Rev=1 Len=024
Kernel driver in use: nvidia
Kernel modules: nvidia, nouveau, nvidiafb
Even though there is now a driver in use (installed from here:
) I still cannot adjust my resolution. I didn't install nVidia's own driver because of this article: There is only ONE resolution in the display settings (1024X768). Attaching an external monitor results in the computer shutting down on its own. And there is no way to adjust brightness.
Aarrgh. Frustration ++. I am just going to ignore this today. I have too much work piled up.
tinypliny - 10/17/11 15:21
Even better commands (thanks to (e:paul))
sudo geany /var/log/yum.log - just shows you a log of everything ordered by name
to order the last command
rpm -qa --queryformat '%{NAME}%{VERSION}%{RELEASE} was installed on %{INSTALLTIME:date}\n' --last
the --last works just as well as sorting
Even better commands (thanks to (e:paul))
sudo geany /var/log/yum.log - just shows you a log of everything ordered by name
to order the last command
rpm -qa --queryformat '%{NAME}%{VERSION}%{RELEASE} was installed on %{INSTALLTIME:date}\n' --last
the --last works just as well as sorting
tinypliny - 10/17/11 13:16
Better tracking: rpm -qa --queryformat '%{NAME}%{VERSION}%{RELEASE} was installed on %{INSTALLTIME:date}\n' > package
Better tracking: rpm -qa --queryformat '%{NAME}%{VERSION}%{RELEASE} was installed on %{INSTALLTIME:date}\n' > package
tinypliny - 10/17/11 13:09
Got it!! rpm -qa --queryformat '%{NAME} was installed on %{INSTALLTIME:date}\n'
Got it!! rpm -qa --queryformat '%{NAME} was installed on %{INSTALLTIME:date}\n'
uncutsaniflush - 10/17/11 09:24
As a general rule, it is a good idea to update after an fresh install unless you have a specific reason not to. Some installers will do it for you. Sometimes you will end up with library, kernel, and/or dependency problems if you only update/install specific apps without doing a general update.
As to upgrading from one version of a distro to new one, I always perfer to do a fresh install of the new version instead of an "update" install. As to updating to a new version from inside a distro, it all depends. I don't have a general rule.
If nouveau is working you don't need nvidiafb. At the very least blacklist it. Also remember that you shouldn't have nvidia and nvidiafb at the same time. They don't like each other and do not play nice.
The brightness thing may be a permission thing since the settings only work for a session. You may need to add your user to the admin or wheel or something like that.
As a general rule, it is a good idea to update after an fresh install unless you have a specific reason not to. Some installers will do it for you. Sometimes you will end up with library, kernel, and/or dependency problems if you only update/install specific apps without doing a general update.
As to upgrading from one version of a distro to new one, I always perfer to do a fresh install of the new version instead of an "update" install. As to updating to a new version from inside a distro, it all depends. I don't have a general rule.
If nouveau is working you don't need nvidiafb. At the very least blacklist it. Also remember that you shouldn't have nvidia and nvidiafb at the same time. They don't like each other and do not play nice.
The brightness thing may be a permission thing since the settings only work for a session. You may need to add your user to the admin or wheel or something like that.
tinypliny - 10/17/11 08:36
Do you do a complete update every time you install a distribution? sudo yum update? Or do you let things be if they are running fine after the fresh install?
Do you do a complete update every time you install a distribution? sudo yum update? Or do you let things be if they are running fine after the fresh install?
tinypliny - 10/17/11 08:15
Not going back to xfce version even though gnome 3 is a pain to deal with (for me). A working stable environment is way more important than a few inconveniences.
Not going back to xfce version even though gnome 3 is a pain to deal with (for me). A working stable environment is way more important than a few inconveniences.
tinypliny - 10/17/11 08:13
thanks, taking all your advice. Is this the correct virtual box site? :::link:::
(e:uncut): I tried the live gnome cd and this is the output:
01:00.0 VGA compatible controller [0300]: nVidia Corporation Device [10de:0df4] (rev a1) (prog-if 00 [VGA controller])
Subsystem: Toshiba America Info Systems Device [1179:fc31]
Flags: bus master, fast devsel, latency 0, IRQ 16
Memory at f6000000 (32-bit, non-prefetchable) [size=16M]
Memory at e0000000 (64-bit, prefetchable) [size=256M]
Memory at f0000000 (64-bit, prefetchable) [size=32M]
I/O ports at e000 [size=128]
Expansion ROM at f7000000 [disabled] [size=512K]
Capabilities: [60] Power Management version 3
Capabilities: [68] MSI: Enable- Count=1/1 Maskable- 64bit+
Capabilities: [78] Express Endpoint, MSI 00
Capabilities: [b4] Vendor Specific Information: Len=14
Capabilities: [100] Virtual Channel
Capabilities: [128] Power Budgeting
Capabilities: [600] Vendor Specific Information: ID=0001 Rev=1 Len=024
Kernel driver in use: nouveau
Kernel modules: nouveau, nvidiafb
Brightness and external monitors work but brightness settings are never remembered.
I didn't try the fedora live xfce version because I had to wipe it out to put the gnome version on (I lost a couple usbs recently so I am running short of spare ones).
thanks, taking all your advice. Is this the correct virtual box site? :::link:::
(e:uncut): I tried the live gnome cd and this is the output:
01:00.0 VGA compatible controller [0300]: nVidia Corporation Device [10de:0df4] (rev a1) (prog-if 00 [VGA controller])
Subsystem: Toshiba America Info Systems Device [1179:fc31]
Flags: bus master, fast devsel, latency 0, IRQ 16
Memory at f6000000 (32-bit, non-prefetchable) [size=16M]
Memory at e0000000 (64-bit, prefetchable) [size=256M]
Memory at f0000000 (64-bit, prefetchable) [size=32M]
I/O ports at e000 [size=128]
Expansion ROM at f7000000 [disabled] [size=512K]
Capabilities: [60] Power Management version 3
Capabilities: [68] MSI: Enable- Count=1/1 Maskable- 64bit+
Capabilities: [78] Express Endpoint, MSI 00
Capabilities: [b4] Vendor Specific Information: Len=14
Capabilities: [100] Virtual Channel
Capabilities: [128] Power Budgeting
Capabilities: [600] Vendor Specific Information: ID=0001 Rev=1 Len=024
Kernel driver in use: nouveau
Kernel modules: nouveau, nvidiafb
Brightness and external monitors work but brightness settings are never remembered.
I didn't try the fedora live xfce version because I had to wipe it out to put the gnome version on (I lost a couple usbs recently so I am running short of spare ones).
uncutsaniflush - 10/16/11 23:04
I concur with (e:paul). but still I would run the live fedora (be it xfce or gnome) to confirm that the nouveux driver works before doing a reinstall. But I tend to trust (e:paul) that it would work.
I concur with (e:paul). but still I would run the live fedora (be it xfce or gnome) to confirm that the nouveux driver works before doing a reinstall. But I tend to trust (e:paul) that it would work.
paul - 10/16/11 22:57
I wouldn't even play with the nvidia drivers as nouveux should be working fine for what you need.
Here is my advice. Reinstall Fedora, install virtual box from the oracle site. Install another copy of fedora in there. Test anything in the virtual fedora before you apply to the real fedora. That way you won't keep messing up your comp and can continue to work.
I wouldn't even play with the nvidia drivers as nouveux should be working fine for what you need.
Here is my advice. Reinstall Fedora, install virtual box from the oracle site. Install another copy of fedora in there. Test anything in the virtual fedora before you apply to the real fedora. That way you won't keep messing up your comp and can continue to work.
uncutsaniflush - 10/16/11 22:53
Ok, here's my advice, run Fedora-xfce live. If it works, you know it is something you installed post-install that is fucking up your system. Look at what kernel modules are loaded. If the live cd works, make sure only that module is loaded on your installed system.
When you installed did you do a fresh install or an update? to put in other words, did you format your root partition before installing fedora-xfce? If you didn't everything from the old install is probably still floating around.
Ok, here's my advice, run Fedora-xfce live. If it works, you know it is something you installed post-install that is fucking up your system. Look at what kernel modules are loaded. If the live cd works, make sure only that module is loaded on your installed system.
When you installed did you do a fresh install or an update? to put in other words, did you format your root partition before installing fedora-xfce? If you didn't everything from the old install is probably still floating around.
uncutsaniflush - 10/16/11 22:37
My experience is that you can't have both the nvidia and the nouveau kernel modules loaded at the same time without bad shit happening.
Somehow you managed to install nvidia kernel modules from somewhere. At the very least blacklist one or the other.
Nothing that you installed with :::link::: should have kernel module graphics drivers. I'm with (e:paul) on that.
My experience is that you can't have both the nvidia and the nouveau kernel modules loaded at the same time without bad shit happening.
Somehow you managed to install nvidia kernel modules from somewhere. At the very least blacklist one or the other.
Nothing that you installed with :::link::: should have kernel module graphics drivers. I'm with (e:paul) on that.
tinypliny - 10/16/11 22:09
Its just a theory though. In addition, I added
-- texmaker
-- texstudio
-- gnumeric
-- pinta
Its just a theory though. In addition, I added
-- texmaker
-- texstudio
-- gnumeric
-- pinta
paul - 10/16/11 22:05
Okay, thats crazy. Something else must have been installed. The mp3 codecs have nothing to do with the display driver.
Okay, thats crazy. Something else must have been installed. The mp3 codecs have nothing to do with the display driver.
tinypliny - 10/16/11 22:05
I think the mp3 and other codecs caused the nvidia card Optimus thingy to kick in and this stalled the OS. It's my theory, because the error screen was only intermittent before. But after the codecs, it just stalled the entire OS from booting.
I think the mp3 and other codecs caused the nvidia card Optimus thingy to kick in and this stalled the OS. It's my theory, because the error screen was only intermittent before. But after the codecs, it just stalled the entire OS from booting.
tinypliny - 10/16/11 22:03
Nope. It stalled in the black screen of death after I put in the mp3 codecs. I couldn't rescue it so I put in fedora xfce. This is the state after fedora xfce.
Nope. It stalled in the black screen of death after I put in the mp3 codecs. I couldn't rescue it so I put in fedora xfce. This is the state after fedora xfce.
paul - 10/16/11 21:48
How did you get it to this point. It was not like this originally from your bro, was it?
How did you get it to this point. It was not like this originally from your bro, was it?
10/17/2011 19:29 #55328
[Solved] External Monitor problems on Fedora 15Category: linux
Found a nice solution to the crazy external monitor problem in Fedora 15:
Download the latest release of ARandR from here:
Extract to some directory and navigate to that directory:
Run arandr.
All external display problems SOLVED! Woohoo. Thank you, Christian Amsuess. You simply rock. I saw they are trying to get this nifty program reviewed to include it in the Fedora yum repository For such a wonderful program that replaces the crap they have in gnome 3, the brutal review process seems somewhat counterproductive.
The Extended monitor display works. However, if I assign the external monitor as the primary display, it doesn't work. It gives me a blank backlit screen. WHYYYY?
I really need one of these counters now.
The number matches. I have the exact expression too.
In addition, I feel like I could outshout the incredible hulk anytime after /var/log/messages records an exception that could have well read, "You wouldn't like me when I'mangry normal".
Last few lines from /var/log/Xorg.0.log
Download the latest release of ARandR from here:
Extract to some directory and navigate to that directory:
cd /arandr-0.1.5/
Run arandr.
./arandr
All external display problems SOLVED! Woohoo. Thank you, Christian Amsuess. You simply rock. I saw they are trying to get this nifty program reviewed to include it in the Fedora yum repository
For such a wonderful program that replaces the crap they have in gnome 3, the brutal review process seems somewhat counterproductive.The Extended monitor display works. However, if I assign the external monitor as the primary display, it doesn't work. It gives me a blank backlit screen. WHYYYY?
I really need one of these counters now.
The number matches. I have the exact expression too.
In addition, I feel like I could outshout the incredible hulk anytime after /var/log/messages records an exception that could have well read, "You wouldn't like me when I'm
Last few lines from /var/log/Xorg.0.log
[ 2244.948] (II) intel(0): EDID vendor "HWP", prod id 9896
[ 2244.948] (II) intel(0): Using hsync ranges from config file
[ 2244.948] (II) intel(0): Using vrefresh ranges from config file
[ 2244.948] (II) intel(0): Printing DDC gathered Modelines:
[ 2244.948] (II) intel(0): Modeline "1680x1050"x0.0 146.25 1680 1784 1960 2240 1050 1053 1059 1089 -hsync +vsync (65.3 kHz)
[ 2244.948] (II) intel(0): Modeline "800x600"x0.0 40.00 800 840 968 1056 600 601 605 628 +hsync +vsync (37.9 kHz)
[ 2244.948] (II) intel(0): Modeline "640x480"x0.0 31.50 640 656 720 840 480 481 484 500 -hsync -vsync (37.5 kHz)
[ 2244.948] (II) intel(0): Modeline "640x480"x0.0 25.18 640 656 752 800 480 490 492 525 -hsync -vsync (31.5 kHz)
[ 2244.948] (II) intel(0): Modeline "720x400"x0.0 28.32 720 738 846 900 400 412 414 449 -hsync +vsync (31.5 kHz)
[ 2244.948] (II) intel(0): Modeline "1280x1024"x0.0 135.00 1280 1296 1440 1688 1024 1025 1028 1066 +hsync +vsync (80.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1024x768"x0.0 78.75 1024 1040 1136 1312 768 769 772 800 +hsync +vsync (60.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1024x768"x0.0 65.00 1024 1048 1184 1344 768 771 777 806 -hsync -vsync (48.4 kHz)
[ 2244.948] (II) intel(0): Modeline "832x624"x0.0 57.28 832 864 928 1152 624 625 628 667 -hsync -vsync (49.7 kHz)
[ 2244.948] (II) intel(0): Modeline "800x600"x0.0 49.50 800 816 896 1056 600 601 604 625 +hsync +vsync (46.9 kHz)
[ 2244.948] (II) intel(0): Modeline "1152x864"x0.0 108.00 1152 1216 1344 1600 864 865 868 900 +hsync +vsync (67.5 kHz)
[ 2244.948] (II) intel(0): Modeline "1152x720"x60.0 67.32 1152 1208 1328 1504 720 721 724 746 -hsync +vsync (44.8 kHz)
[ 2244.948] (II) intel(0): Modeline "1280x960"x0.0 108.00 1280 1376 1488 1800 960 961 964 1000 +hsync +vsync (60.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1440x900"x0.0 106.50 1440 1520 1672 1904 900 903 909 934 -hsync +vsync (55.9 kHz)
[ 2244.948] (II) intel(0): Modeline "1600x1000"x60.0 133.14 1600 1704 1872 2144 1000 1001 1004 1035 -hsync +vsync (62.1 kHz)
[ 2261.254] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2261.254] (II) intel(0): Printing DDC gathered Modelines:
[ 2261.254] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.258] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2262.258] (II) intel(0): Printing DDC gathered Modelines:
[ 2262.258] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.353] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2262.353] (II) intel(0): Printing DDC gathered Modelines:
[ 2262.353] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.467] (II) intel(0): Allocated new frame buffer 1728x1050 stride 7168, tiled
[ 2293.167] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2293.167] (II) intel(0): Printing DDC gathered Modelines:
[ 2293.167] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2293.280] (II) intel(0): Allocated new frame buffer 3072x1050 stride 12288, tiled
Nice....