Lindqvist - a blog about Linux and Science. Mostly.
sudo apt-get install bkchem
sh marvinbeans-6.1.0-linux_with_jre64.sh
[Desktop Entry] Name=MarvinSketch GenericName=MarvinSketch Comment=Software for drawing molecules Exec=sh /home/me/ChemAxon/MarvinBeans/MarvinSketch Terminal=false Type=Application Categories=Science Version=6.1
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| A Blank slate |
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| Running Chem Inspector |
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| It didn't like my wedges |
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| I turned the structure into 3D and rotated it |
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| Elemental analysis |
sudo dpkg --add-architecture sudo apt-get update sudo apt-get install wine:i386 wget http://fc.smcdsb.on.ca/~rszerminski/addl_files_for_web/DRAW24.EXE wine DRAW24.EXE
wget http://winetricks.org/winetricks sudo mv winetricks /usr/bin/winetricks chmod +x /usr/bin/winetricks winetricks allfonts
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| A blank slate |
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| Chem Inspector |
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| To get the menus to work, click and while still holding the left button down move right |
sudo apt-get autoremove wps-office:i386
mkdir ~/tmp cd ~/tmp sudo dpkg --add-architecture i386 sudo apt-get update wget http://wdl.cache.ijinshan.com/wps/download/Linux/unstable/kingsoft-office_9.1.0.4244~a12p3_i386.deb sudo dpkg -i kingsoft-office_9.1.0.4244~a12p3_i386.deb sudo apt-get install -f
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| Missing fonts. Clicking on the link takes you indirectly to bbs.wpn.cn, which is in Chinese. |
cp ~/Downloads/wps_symbol_fonts.zip ~/.fonts cd ~/.fonts unzip wps_symbol_fonts.zip
sudo update-desktop-database /usr/local/share/applications/ sudo update-mime-database /usr/share/mime/
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| The new behaviour |
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| Check 'Sort folders before files' to get back the normal behaviour |
me@beryllium:~/Downloads$ lpstat
global-mfp-1166 me 591872 Mon 11 Nov 2013 12:36:29 EST
global-mfp-1167 me 993280 Mon 11 Nov 2013 12:36:44 EST
global-mfp-1168 me 2014208 Mon 11 Nov 2013 12:36:59 EST
global-mfp-1169 me 871424 Mon 11 Nov 2013 12:37:17 EST
global-mfp-1170 me 573440 Mon 11 Nov 2013 12:37:31 EST
global-mfp-1171 me 1199104 Mon 11 Nov 2013 12:37:51 EST
global-mfp-1172 me 183296 Mon 11 Nov 2013 12:38:02 EST
global-mfp-1173 me 491520 Mon 11 Nov 2013 12:38:19 EST
global-mfp-1174 me 2035712 Mon 11 Nov 2013 12:38:38 EST
global-mfp-1175 me 2035712 Mon 11 Nov 2013 12:39:54 EST
global-mfp-1176 me 635904 Mon 11 Nov 2013 12:41:54 EST
global-mfp-1177 me 148480 Mon 11 Nov 2013 16:29:58 EST
I preceded to cancel all the jobs:
me@beryllium:~/Downloads$ cancel global-mfp-1166
me@beryllium:~/Downloads$ lpstat
global-mfp-1167 me 993280 Mon 11 Nov 2013 12:36:44 EST
global-mfp-1168 me 2014208 Mon 11 Nov 2013 12:36:59 EST
global-mfp-1169 me 871424 Mon 11 Nov 2013 12:37:17 EST
global-mfp-1170 me 573440 Mon 11 Nov 2013 12:37:31 EST
global-mfp-1171 me 1199104 Mon 11 Nov 2013 12:37:51 EST
global-mfp-1172 me 183296 Mon 11 Nov 2013 12:38:02 EST
global-mfp-1173 me 491520 Mon 11 Nov 2013 12:38:19 EST
global-mfp-1174 me 2035712 Mon 11 Nov 2013 12:38:38 EST
global-mfp-1175 me 2035712 Mon 11 Nov 2013 12:39:54 EST
global-mfp-1176 me 635904 Mon 11 Nov 2013 12:41:54 EST
global-mfp-1177 me 148480 Mon 11 Nov 2013 16:29:58 EST
me@beryllium:~/Downloads$ cancel global-mfp-1167
me@beryllium:~/Downloads$ cancel global-mfp-1168
me@beryllium:~/Downloads$ cancel global-mfp-1169
me@beryllium:~/Downloads$ cancel global-mfp-1170
me@beryllium:~/Downloads$ cancel global-mfp-1171
me@beryllium:~/Downloads$ cancel global-mfp-1172
me@beryllium:~/Downloads$ cancel global-mfp-1173
me@beryllium:~/Downloads$ cancel global-mfp-1174
me@beryllium:~/Downloads$ cancel global-mfp-1175
me@beryllium:~/Downloads$ cancel global-mfp-1176
me@beryllium:~/Downloads$ cancel global-mfp-1177
me@beryllium:~/Downloads$ lpstat
me@beryllium:~/Downloads$
andStill only a 4+1 phase board the FX chips pull a bit more power than that can put out comfortably and stable. [..] Those would be your three best to choose from all are the better 8+2 phase designs...
my opinion is to stay away from the asus FX ive seen many people asking why their boards are throttling at full load, vrm protection causes voltages to drop at full load when vrms hit a certain temp.
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| Case, closed |
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| The glorious innards of The Case. |
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| The 700GX does not come with a mobo panel -- not that they tend to be useful anyway |
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| Luckily all (most?) mobos come with their own panels -- push it in place before doing anything else. It can need a bit of negotiation in order to snap in properly. |
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| The case came with riser nuts, four PSU screws and lots of screws for the mobo. |
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| Put the riser nuts in the case -- they are the golden thingies |
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| And here's the mother board. I don't know if there are universally accepted recommendations, but I prefer to install the CPU and RAM onto the mother board before installing it in the case -- you have more space to manouver and the risk of breaking the board is smaller. |
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| The heatsink (left) and CPU (right) |
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| The heatsink comes with thermal paste pre-applied. Don't touch it -- you want it to be as smooth and even as possible. |
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| Get the CPU out |
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| Note the yellow triangle in the bottom right corner in the picture |
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| That should match up with the triangle in the bottom left of this picture. Note the raised level on the right side of the CPU socket. |
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| The CPU in place. Note the raised lever. There should be no pushing -- the CPU should fit perfectly without any force whatsoever. If you bend a pin...then good luck. |
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| The lever is in the locked position. |
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| Next put the heatsink on. Give this a bit of thought as you won't want to have to reseat it several times (in the worst case you'll have to go buy some thermal paste, clean the heatsink and reapply the paste). So make sure you line up the fasteners before pushing the heatsink in place. |
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| Everything is locked down. |
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| The motherboard with the processor and heatsink in place. In the picture the CPU fan is attached to the WRONG connector. Look for a connector saying 'CPU FAN' (in the picture it's attached to POWER FAN) |
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| Open the RAM slot fasteners, and push the RAM sticks in place firmly, but without excessive violence. Once the fasteners snap shut by themselves the sticks are properly seated. Improperly seated RAM sticks tend to prevent you from booting and leads to a lot of noise. |
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| All four RAM sticks in place, and the motherboard attached to the case via seven screws that screw into the riser nuts. |
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| The PSU is in place. |
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| Main power and auxiliary power cables attached. |
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| This particular case has a special tray for the hard drives. |
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| Hard drive in place |
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| SATA data and power cables attached |
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| The other end of the SATA data cable attaches to the motherboard (SATA 1) |
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| After a bit of rewiring. |
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| PCI NIC and PCI-E graphics cards in place. |
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set number set pastetoggle=<f3> nnoremap <f4> :set nonumber!<CR>
sudo update-alternatives --config editor
I set up 'static' dhcp on the WAN router.OPTS="${OPTS} --quiet --bcastaddress=192.168.1.255"
auto lo iface lo inet loopback auto eth1 iface eth1 inet dhcp auto eth0 iface eth0 inet static address 192.168.1.180 gateway 192.168.1.1 netmask 255.255.255.0 post-up ip route flush all post-up route add default eth1 post-up route add -net 192.168.1.0 netmask 255.255.255.0 gw 192.168.1.1 eth0
127.0.0.1 localhost #127.0.1.1 oxygen 192.168.1.180 oxygen
mkdir ~/oxygen mkdir ~/scratch chmod 777 ~/oxygen
ssh-keygen vim ~/.ssh/authorized_keys
mkdir ~/tmp/mprime -p cd ~/tmp/mprime wget http://www.mersenne.info/gimps/p95v279.linux64.tar.gz tar xvf p95v279.linux64.tar.gz ./mprimeAnd so on.Welcome to GIMPS, the hunt for huge prime numbers. You will be asked a few simple questions and then the program will contact the primenet server to get some work for your computer. Good luck! Attention OVERCLOCKERS!! Mprime has gained a reputation as a useful stress testing tool for people that enjoy pushing their hardware to the limit. You are more than welcome to use this software for that purpose. Please select the stress testing choice below to avoid interfering with the PrimeNet server. Use the Options/Torture Test menu choice for your stress tests. Also, read the stress.txt file. If you want to both join GIMPS and run stress tests, then Join GIMPS and answer the questions. After the server gets some work for you, stop mprime, then run mprime -m and choose Options/Torture Test. Join Gimps? (Y=Yes, N=Just stress testing) (Y): N Number of torture test threads to run (3): 2 Choose a type of torture test to run. 1 = Small FFTs (maximum FPU stress, data fits in L2 cache, RAM not tested much). 2 = In-place large FFTs (maximum heat and power consumption, some RAM tested). 3 = Blend (tests some of everything, lots of RAM tested). 11,12,13 = Allows you to fine tune the above three selections. Blend is the default. NOTE: if you fail the blend test, but can pass the small FFT test then your problem is likely bad memory or a bad memory controller. Type of torture test to run (3): 1 Accept the answers above? (Y): Y [Main thread Sep 20 11:06] Starting workers. [Worker #1 Sep 20 11:06] Worker starting [Worker #1 Sep 20 11:06] Setting affinity to run worker on any logical CPU. [Worker #2 Sep 20 11:06] Worker starting [Worker #2 Sep 20 11:06] Setting affinity to run worker on any logical CPU. [Worker #1 Sep 20 11:06] Beginning a continuous self-test to check your computer. [Worker #1 Sep 20 11:06] Please read stress.txt. Hit ^C to end this test. [Worker #2 Sep 20 11:06] Beginning a continuous self-test to check your computer. [Worker #2 Sep 20 11:06] Please read stress.txt. Hit ^C to end this test. [Worker #1 Sep 20 11:06] Test 1, 180000 Lucas-Lehmer iterations of M580673 using AMD K10 type-1 FFT length 28K, Pass1=112, Pass2=256. [Worker #2 Sep 20 11:06] Test 1, 180000 Lucas-Lehmer iterations of M580673 using AMD K10 type-1 FFT length 28K, Pass1=112, Pass2=256. CTRL+C
mkdir ~/tmp cd ~/tmp cp ~/Downloads/l_mkl_11.0.4.183.tgz . tar xvf l_mkl_11.0.4.183.tgz cd l_mkl_11.0.4.183 sudo sh install.shStep no: 1 of 7 | Welcome -------------------------------------------------------------------------------- Welcome to the Intel(R) Math Kernel Library 11.0 Update 4 for Linux* installation program. The Flagship of HPC Math Libraries. This library contains highly optimized, extensively threaded, mathematical functions for engineering, scientific, and financial applications that require maximum performance. -------------------------------------------------------------------------------- You will complete the steps below during this installation: Step 1 : Welcome Step 2 : License Step 3 : Activation Step 4 : Intel(R) Software Improvement Program Step 5 : Options Step 6 : Installation Step 7 : Complete -------------------------------------------------------------------------------- Step no: 1 of 7 | Options > Missing Optional Pre-requisite(s) -------------------------------------------------------------------------------- There are one or more optional unresolved issues. It is highly recommended to resolve them all before you continue the installation. You can fix them without exiting from the installation and re-check. Or you can quit from the installation, fix them and run the installation again. -------------------------------------------------------------------------------- Missing optional pre-requisites -- unsupported OS -------------------------------------------------------------------------------- 1. Skip missing optional pre-requisites [default] 2. Show the detailed info about issue(s) 3. Re-check the pre-requisites h. Help b. Back to the previous menu q. Quit -------------------------------------------------------------------------------- Please type a selection or press "Enter" to accept default choice [1]: 1 [..] 13. THIRD PARTY PROGRAMS. The Materials may include third party programs or materials that are governed by the third party's license terms, including without limitation, open source software. The license terms associated with such third party programs or materials govern your use of same, and Intel is not liable for such third party programs or materials. * Other names and brands may be claimed as the property of others -------------------------------------------------------------------------------- Do you agree to be bound by the terms and conditions of this license agreement? Type "accept" to continue or "decline" to back to the previous menu: accept Step no: 3 of 7 | Activation -------------------------------------------------------------------------------- If you have purchased this product and have the serial number and a connection to the internet you can choose to activate the product at this time. Activation is a secure and anonymous one-time process that verifies your software licensing rights to use the product. Alternatively, you can choose to evaluate the product or defer activation by choosing the evaluate option. Evaluation software will time out in about one month. Also you can use license file, license manager, or remote activation if the system you are installing on does not have internet access activation options. -------------------------------------------------------------------------------- 1. I want to activate my product using a serial number [default] 2. I want to evaluate my product or activate later 3. I want to activate either remotely, or by using a license file, or by using a license manager h. Help b. Back to the previous menu q. Quit -------------------------------------------------------------------------------- Please type a selection or press "Enter" to accept default choice [1]: 1 Note: Press "Enter" key to back to the previous menu. Please type your serial number (the format is XXXX-XXXXXXXX): -------------------------------------------------------------------------------- Activation completed successfully. -------------------------------------------------------------------------------- Press "Enter" key to continue: Step no: 4 of 7 | Intel(R) Software Improvement Program -------------------------------------------------------------------------------- Help improve your experience with Intel(R) software Participate in the design of future Intel software. Select 'Yes' to give us permission to learn about how you use your Intel software and we will do the rest. - No Personal contact information is collected - There are no surveys or additional follow-up emails by opting in - You can stop participating at any time Learn more about Intel(R) Software Improvement Program http://software.intel.com/en-us/articles/software-improvement-program With your permission, Intel may automatically receive anonymous information about how you use your current and future Intel software. -------------------------------------------------------------------------------- 1. Yes, I am willing to participate and improve Intel software. (Recommended) 2. No, I don't want to participate in the Intel(R) Software Improvement Program at this time. b. Back to the previous menu q. Quit -------------------------------------------------------------------------------- Please type a selection: 2 Step no: 5 of 7 | Options -------------------------------------------------------------------------------- You are now ready to begin installation. You can use all default installation settings by simply choosing the "Start installation Now" option or you can customize these settings by selecting any of the change options given below first. You can view a summary of the settings by selecting "Show pre-install summary". -------------------------------------------------------------------------------- 1. Start installation Now 2. Change install directory [ /opt/intel/composer_xe_2013.4.183 ] 3. Change components to install [ All ] 4. Show pre-install summary h. Help b. Back to the previous menu q. Quit -------------------------------------------------------------------------------- Please type a selection or press "Enter" to accept default choice [1]: 1 Step no: 6 of 7 | Installation -------------------------------------------------------------------------------- Each component will be installed individually. If you cancel the installation, components that have been completely installed will remain on your system. This installation may take several minutes, depending on your system and the options you selected. -------------------------------------------------------------------------------- Installing Intel Math Kernel Library 11.0 Update 4 on IA-32 component... done -------------------------------------------------------------------------------- Installing Intel Math Kernel Library 11.0 Update 4 on Intel(R) 64 component... done -------------------------------------------------------------------------------- Finalizing installation... done -------------------------------------------------------------------------------- Press "Enter" key to continue Step no: 7 of 7 | Complete -------------------------------------------------------------------------------- Thank you for installing and for using the Intel(R) Math Kernel Library 11.0 Update 4 for Linux*. Support services start from the time you install or activate your product, so please create your support account now in order to take full advantage of your product purchase. Your Subscription Service support account provides access to free product updates interactive issue management, technical support, sample code, and documentation. To create your support account, please visit the Subscription Services web site https://registrationcenter.intel.com/RegCenter/registerexpress.aspx?clientsn=NBJ N-87S2RM3P To get started using Intel(R) Math Kernel Library 11.0 Update 4 located in /opt/intel/composer_xe_2013.4.183 visit: install-dir/Documentation/en_US/mkl/get_started.html. -------------------------------------------------------------------------------- q. Quit [default] -------------------------------------------------------------------------------- Please type a selection or press "Enter" to accept default choice [q]:
sudo apt-get install build-essential gfortran python2.7-dev libopenmpi-dev openmpi-bin sudo mkdir /opt/nwchem -p sudo chown $USER:$USER /opt/nwchem cd /opt/nwchem wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.3.revision1-src.2013-05-28.tar.gz -O Nwchem-6.3.revision1-src.2013-05-28.tar.gz tar xvf Nwchem-6.3.revision1-src.2013-05-28.tar.gz cd nwchem-6.3-src.2013-05-28/ export NWCHEM_TOP=`pwd` export LARGE_FILES=TRUE export TCGRSH=/usr/bin/ssh export NWCHEM_TOP=`pwd` export NWCHEM_TARGET=LINUX64 export NWCHEM_MODULES="all python" export PYTHONVERSION=2.7 export PYTHONHOME=/usr export BLASOPT="-L/opt/intel/composer_xe_2013.4.183/mkl/lib/intel64/ -lmkl_sequential -lmkl_core -lmkl_intel_ilp64" export LIBRARY_PATH="$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/intel/composer_xe_2013.4.183/mkl/lib/intel64/" export USE_MPI=y export USE_MPIF=y export USE_MPIF4=y export MPI_LOC=/usr/lib/openmpi/lib export MPI_INCLUDE=/usr/lib/openmpi/include export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread" export ARMCI_NETWORK=SOCKETS cd $NWCHEM_TOP/src make clean make nwchem_config make FC=gfortran 1> make.log 2>make.err cd $NWCHEM_TOP/contrib export FC=gfortran ./getmem.nwchem
219183542ada47a17e5528bf217f9261 anode.bz2 61335e6b9cf2e654242db80822f32681 ciftab.bz2 918fe0a04e59589938a81a93d8e3eaff shelxc.bz2 e65580af087989aa4958eb53dcd8a473 shelxd.bz2 bc5cad6e4129fa61bbde49207cd4d244 shelxe.bz2 5390146a4b516425fb7b326533443ba7 shelxl.bz2 95617863be917743df55bd94509504fb shelxs.bz2
sudo apt-get install bunzip2 xargs
mkdir ~/tmp/shelx-2013 -p
cd ~/Downloads
cp shredcif.bz2 shelxe.bz2 shelxd.bz2 shelxc.bz2 ciftab.bz2 anode.bz2 shelxl.bz2 shelxs.bz2 ~/tmp/shelx-2013
cd ~/tmp/shelx-2013/
ls *.bz2|xargs -I {} bunzip2 {}
chmod +x *
sudo cp * /usr/local/bin
mkdir ~/tmp/shelx_examples
cd ~/Downloads
cp cdetutorial_andrea.zip ciftab_templates.zip difficult_sad.zip ltests.zip pn1a.zip ~/tmp/shelx_examples
cd ~/shelx_examples
ls *.zip |xargs -I {} unzip {}