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  • SAS and Python, SASPy, SAS_Kernel for Jupyter Notebook SAS Programming for R Users (Course Materials) SAS environments outside of SAS University Edition, here's what you need to ...
    Posted Mar 27, 2018, 6:23 PM by Dong Xu
  • Log compilation, installation steps ./configure --prefix=/home/you/mpich-install  2>&1 | tee config.log  (bash)|& tee (csh)make VERBOSE=1 |& tee make.log (for csh and tcsh) make VERBOSE=1 2>&1 | tee ...
    Posted Feb 15, 2018, 9:27 AM by Dong Xu
  • Linux hardware info sudo /usr/sbin/dmidecodFor details:
    Posted Feb 14, 2018, 2:45 PM by Dong Xu
  • M.2 drive SSD vs NVMe Are all M.2 drives NVMe? No. Remember, M.2 is just the form factor. M.2 drives can come in SATA versions (like the Crucial MX300 M.2 for ...
    Posted Feb 7, 2018, 11:13 AM by Dong Xu
  • View and convert SVG file on Linux and Windows On SUSE, install rsvg-view from yast2Viewer:  rsvg-view-3 filename.svgConverter:  -f, --format=[png, pdf, ps, eps, svg, xml, recording] rsvg-convert C2-C1-C3-C6.svg ...
    Posted Feb 6, 2018, 10:58 AM by Dong Xu
  • Sqlite vs MySQL
    Posted Jan 14, 2018, 5:21 PM by Dong Xu
  • tar to stdout tar xvf archive.tar -O | lesstar xvf archive.tar -O | grep [ ]For a file inside tar filetar xvf archive.tar file_with_path -O | lesstar xvf archive ...
    Posted Jan 10, 2018, 9:07 PM by Dong Xu
  • CXX11 compilation error If you get linker errors about undefined references to symbols that involve types in the std::__cxx11 namespace or ...
    Posted Jan 6, 2018, 10:00 AM by Dong Xu
  • Amber16 + AmberTool17 installation sudo conda create -n amber16 python=2.7install the following packages:numpymatplotlibscipyipythonnotebookcythonsudo yast2install  libbz2-1 libbz2-develexport AMBERHOME=/garlic/apps/Downloads ...
    Posted Feb 15, 2018, 3:46 PM by Dong Xu
  • MDL Mol/SDF V2000 vs V3000 Most apps: obabel, ChemAxon etc. can handle the conversion: ...
    Posted Dec 24, 2017, 3:31 PM by Dong Xu
  • CMake find OpenBabel installed in Conda The magic line is in cmake/modules/FindOpenBabel2.cmake                NAMES                        openbabel/obconversion.h                        openbabel-2.0/openbabel/obconversion.h
    Posted Dec 21, 2017, 1:17 PM by Dong Xu
  • Install gnina and Caffe clone cd gninaTip: vi CMakeCache.txt to debugCreate conda env gnina with python2.7 and install ...
    Posted Jan 5, 2018, 8:09 PM by Dong Xu
  • Minerve2 Backup Procedure 1. login to minerve2 and package all files in your home folder to a tar filenohup tar cvpf minerve2_backup.tar . >& minerve2_backup.log &tail -f minerve2_backup.log ...
    Posted Dec 4, 2017, 4:48 PM by Dong Xu
  • LVM commands on an external eSata/USB3 enclosure Volume Group commands vgscan Scans all the disks for volume groups and rebuilds the LVM cache file, also displays the volume groups. vgchange -a n/y my_volume_group Deactivate ...
    Posted Dec 4, 2017, 2:53 PM by Dong Xu
  • Auto delete Gmail Step 1: Go to Settings -> Filters -> Create a new filter Step 2: Type the following into "Has the words" field: category:promotions older_than:90dor before:2011/01/15 ...
    Posted Dec 3, 2017, 9:16 AM by Dong Xu
  • MongoDB and LINCS L1000 1. Open Robot 3T and click create 2. Fill out connection as shown then hit Authentication tab 3. Check Perform authentication and fill out the fields. The password is dxu123 ...
    Posted Nov 28, 2017, 5:59 PM by Dong Xu
  • Map any key to any key on Windows
    Posted Nov 18, 2017, 10:17 AM by Dong Xu
  • Ginger iptables outbound rules -A OUTPUT -m state --state RELATED,ESTABLISHED -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 22 -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 53 -j ACCEPT-A ...
    Posted Nov 6, 2017, 12:39 PM by Dong Xu
  • Add a Domain name to Google Site Follow instructions here 1 Make sure your domain is using our default name servers. Your domain must be using ...
    Posted Nov 4, 2017, 10:17 AM by Dong Xu
  • Cat concatenate gz files file1.gz file2.gz file3.gz > allfiles-cat.gz zcat file1.gz file2.gz file3.gz | gzip -c > allfiles-zcat.gz zcat allfiles ...
    Posted Oct 26, 2017, 1:30 PM by Dong Xu
  • Windows Subsystem for Linux (WSL), Anaconda, Conda, Jupyter Wow!!! Starting in Windows 10 Anniversary Update, the Windows Subsystem for Linux can invoke native Windows binaries from the Linux console and Linux binaries from a Windows console.  https://msdn ...
    Posted Aug 6, 2018, 1:15 PM by Dong Xu
  • Convert SVG to PNG or JPG  I haven't been able to get good results from ImageMagick in this instance ...
    Posted Oct 24, 2017, 10:26 AM by Dong Xu
  • SCM-ADF uses VTK7 and newer OpenGL features to dramatically speed up the visualization of large systems. This comes with a ...
    Posted Apr 26, 2017, 2:09 PM by Dong Xu
  • Encrypt shell script on Linux and BAT file on Windows Linux ShellHow to: shc: -r -f ./script ...
    Posted Oct 17, 2017, 2:39 PM by Dong Xu
  • Rdkit Cairo Fix for Drawing Molecules from rdkit import Chemfrom rdkit.Chem import AllChemfrom rdkit.Chem import DrawAllChem.Compute2DCoords(m)m = Chem.MolFromSmiles('c1nccc2n1ccc2')Draw.MolToFile(m,'/tmp/test.png')Errors pops up ...
    Posted Apr 18, 2017, 5:00 PM by Dong Xu
  • Linux Cheat Sheet
    Posted Apr 11, 2017, 5:30 PM by Dong Xu
  • Anaconda conda in Schrodinger virtual env ipython='python -m ...
    Posted Sep 18, 2017, 12:46 PM by Dong Xu
  • APC Smart UPS The packages are: apcupsd and apcupsd-gui The status of the daemon can be found with: systemctl status apcupsd.service The graphical interface is: gapcmon And the config file is ...
    Posted Feb 23, 2017, 3:34 PM by Dong Xu
  • Ginger iptables/firewall It's turned on. To change config: vi /etc/iptables/rules.v4
    Posted Jan 30, 2017, 6:34 PM by Dong Xu
  • netcat/nc port scan if a port is opennc -z -v -w5 <host> <port/range>-w5: 5s timeout is optionalExample: nc -zv domain ...
    Posted Nov 2, 2017, 1:20 PM by Dong Xu
  • Firefox 48 update on SLES 12 SP1 Initial update caused breaking of default Gnome Login Screen, the following will prevent it: 1. Open Yast2-->Software-->Software Management 2. Search for firefox 3. Select MozillaFirefox and bring up ...
    Posted Dec 15, 2016, 3:06 PM by Dong Xu
  • awk over ssh all "ps aux|grep virtualgrid|awk '{print \$2}'|head -1|xargs -ti kill {}" all 'nohup virtualgrid -nogui >& virtualgrid_`hostname`.log&'
    Posted Oct 14, 2016, 4:11 PM by Dong Xu
  • Real CPU Load top -b -n2 -p 1 | fgrep "Cpu(s)" | tail -1 | awk -F'id,' -v prefix="$prefix" '{ split($1, vs, ","); v=vs[length(vs)]; sub("%", "", v); printf "%s%.1f%%\n", prefix ...
    Posted Oct 1, 2016, 8:23 PM by Dong Xu
  • Check python unicode version ucs2 vs ucs4 This is for python 2.7When built with --enable-unicode=ucs4: >>> import sys >>> print sys.maxunicode 1114111 When built with --enable-unicode=ucs2: >>> import sys >>> print sys.maxunicode 65535 ...
    Posted Feb 23, 2017, 10:04 AM by Dong Xu
  • Remove python apps installed through “python install” "You need to remove all files manually, and also undo any other stuff that installation did manually. If you don't know the list of all files, you can reinstall ...
    Posted Sep 6, 2016, 11:59 PM by Dong Xu
  • Anaconda env for multi-users!topic/anaconda/qinxkmvlnSg sudo su - adduser anaconda mkdir /opt/anaconda ./path/to/ -b -p /opt/anaconda chown -R anaconda ...
    Posted Sep 6, 2016, 10:03 PM by Dong Xu
  • Monitor Installer/Program Changes in Windows 8 suggested tools suggested tools ...
    Posted Aug 26, 2016, 12:00 PM by Dong Xu
  • SUSE12 clone OS Disk Grub2 ext4 1. Use ddrescue to close to a new disk via USB3. Note that the source OS drive does not need umount2. The new disk should be able to boot ...
    Posted Aug 23, 2016, 5:38 PM by Dong Xu
  • GPU Overclock ...
    Posted Aug 17, 2016, 4:13 PM by Dong Xu
  • GPU fan speed control 1. Do this only onceEnabling Control of Fan Speed and generate xorg.conf file, Adds coolbits to the xorg filesudo nvidia-xconfig -a --cool-bits=28 --allow-empty ...
    Posted Aug 30, 2016, 3:57 PM by Dong Xu
  • Windows 8 AppLocker ...
    Posted Aug 12, 2016, 5:42 PM by Dong Xu
  • Windows 8 NSF NFSv4 Support!! only NFSv3 supportFor v4 support, try UMich program ...
    Posted Aug 12, 2016, 5:48 PM by Dong Xu
  • Windows 8 and 10 Remote Desktop RDP Hack Windows 10 ...
    Posted Mar 27, 2018, 5:54 PM by Dong Xu
  • NVRM: os_schedule: Attempted to yield the CPU while in atomic or interrupt context This is GPU0 Titan Z in peppersee[   26.328777] nvidia-modeset: Loading NVIDIA Kernel Mode Setting Driver for UNIX platforms  361 ...
    Posted Aug 14, 2016, 8:35 AM by Dong Xu
  • File encryption using OpenSSL and PGP Tar the directory tar cvf backup.tar /path/to/folder You can remove the [v] switch from the tar command to switch off the verbose mode. Encrypt openssl aes-256 ...
    Posted Aug 3, 2016, 10:29 AM by Dong Xu
  • Startup scipt for ubuntu 1. simple, requires rootvi /etc/rc.local2. upstart systemA simple command (one which doesn't need to remain running) could use an Upstart job like: start on ...
    Posted Aug 2, 2016, 5:18 PM by Dong Xu
  • Bash commands usage examples: sed, awk etc. #awk one liner one-liner ...
    Posted Oct 8, 2016, 11:10 PM by Dong Xu
  • Well said about GPUs, applicable to computing Always use the latest NVIDIA drivers! (some older versions can cause crashing of FurryBall) Remember, if you will use FurryBall with OLD ...
    Posted Aug 2, 2016, 5:20 PM by Dong Xu
  • BUG: soft lockup - CPU#1 stuck for 22s! [Xorg:2982] Solution: disabling C-states in the BIOS  and other CPU power-saving options such as Turbo Mode/Turbo Boost  etc.. should fix this.Some people also tried adding clocksource=jiffies ...
    Posted Feb 19, 2018, 9:30 AM by Dong Xu
  • Remove an IP address that DenyHosts blocked? /etc/denyhosts.confWORK_DIR=/var/lib/denyhostsIf you have been accidentally locked out of one of your hosts (because DenyHosts has added it to /etc/hosts.deny you ...
    Posted Apr 25, 2017, 3:34 PM by Dong Xu
  • Check Linux distro version, LSB, and diagnose binary file Count number of CPUsgrep -c ^processor /proc/cpuinfo mpstat -P ALL|head -1|cut -d'(' -f3|cut -d')' -f1Distro version (this will also show LSB version): lsb_release ...
    Posted Aug 2, 2016, 4:50 PM by Dong Xu
  • MAC address Start/stop network interfaceOld SUSE ifup, ifdown, ifstatus ...
    Posted Jul 26, 2016, 1:09 AM by Dong Xu
  • Basename ${variable%pattern} Trim the shortest match from the end ${variable##pattern} Trim the longest match from the beginning ${variable%%pattern} Trim the longest match from the end ${variable#pattern} Trim ...
    Posted Jul 22, 2016, 8:23 PM by Dong Xu
  • Passwordless for sudo over ssh 1) sudo vi /etc/sudoers: jenkins ALL=(ALL) NOPASSWD: ALL 2) Put the line after all other lines in the sudoers file! That worked for Ubuntu 14.4 and SUSE12 ...
    Posted Jul 21, 2016, 12:10 AM by Dong Xu
  • Configure sshd openssh you made a change to /etc/ssh/sshd_config you must restart the SSHD or make it reload its configuration by typing ...
    Posted Jul 21, 2016, 12:04 AM by Dong Xu
  • After.local You can also write your scripts and then execute them from /etc/init.d/after.local and /etc/init.d/halt.local The after.local script will be run after ...
    Posted Jul 20, 2016, 7:16 PM by Dong Xu
  • IPTables persistent ...
    Posted Jul 20, 2016, 6:57 PM by Dong Xu
  • Schrodinger Docs Maestro-11 Reference Card ...
    Posted May 28, 2018, 5:15 PM by Dong Xu
  • clusterssh/cssh - multiple host ssh/exec to install package for perlas root cpan -i Tk
    Posted Jul 14, 2016, 4:54 PM by Dong Xu
  • GPU nvidia-smi and Schrodinger Schrodinger:Second, ensure that all your cards have ECC memory turned off, are set to Exclusive Process Mode, and Persistence Mode is on. Disable ECC by running the following command ...
    Posted Aug 11, 2016, 10:10 PM by Dong Xu
  • Disable VMD GPU use You must set the CUDA-related environment variables in your shell prior to launching VMD. In the case of Unix systems, you'd do this: /bin/csh syntax: setenv VMDNOCUDA ...
    Posted Jul 15, 2016, 1:13 PM by Dong Xu
  • IPTables Block IP and IP Range This is the correct way: iptables -A INPUT -p tcp --match multiport --dport 1024:3000 -j ACCEPT As an example. Source here. iptables -A INPUT -p tcp --dport 1000:2000 ...
    Posted Jul 12, 2016, 7:57 AM by Dong Xu
  • SUSE12 Desktop Login Problems 1. If login windows does not show up, press CTRL-ALT-Backspace2. If still doesn't work, login as root, init 3init 5rm /run/nologinOtherwise "System ...
    Posted Jul 11, 2016, 3:34 PM by Dong Xu
  • Fail2ban unban IP   With Fail2Ban before v0.8.8: fail2ban-client get YOURJAILNAMEHERE actionunban IPADDRESSHERE With Fail2Ban v0.8.8 and later: fail2ban-client set YOURJAILNAMEHERE unbanip IPADDRESSHERE The hard part is finding ...
    Posted Jul 12, 2016, 7:46 AM by Dong Xu
  • Xargs ~$ echo 10 20 30 40 50 60 | xargs -n 1 -P 4 sleep The use of “-n 1” is vital if you want to pass only one command-line argument ...
    Posted Jul 9, 2016, 10:12 AM by Dong Xu
  • Super fast backup. copy, move many files To copy a large amount of data, tar is generally faster than rsync. The idea is to start with tar and finish off with a final rsync,tar -cpf - src ...
    Posted Jul 6, 2016, 11:09 PM by Dong Xu
  • Find examples 1. Recursively delete empty directories The find command is the primary tool for recursive, filesystem operations. Use the -type d expression to tell find you're interested in finding directories ...
    Posted Jul 5, 2016, 6:58 PM by Dong Xu
  • Super fast delete a folder with large number of files perl -e 'for(<*>){((stat)[9]<(unlink))}'time find ./ -type f -delete (the BEST)time rsync ...
    Posted Jul 6, 2016, 9:20 AM by Dong Xu
  • Memory editing read: scanmem ...
    Posted Aug 2, 2016, 3:45 PM by Dong Xu
  • White Label hard drives We shoved all the drives in 36 bay Supermicro chassis and LSI 9280 cards and ...
    Posted Jun 24, 2016, 3:04 PM by Dong Xu
  • GPU stress test gpu_burn-0.6.tar.gz (compatible with nvidia-smi and nvcc as of 04-12-2015)This is the best GPU test along with megadock.Note: must run the ...
    Posted Aug 9, 2016, 10:52 AM by Dong Xu
  • SUSE Rescue mode and chroot 1. Start the system with the rescue CD 2. Login with root (no password needed) 3. Mount the / partition. mount /dev/sdc3 /mntmount /dev/sdc1 /mnt/boot4. Give ...
    Posted May 23, 2016, 6:51 PM by Dong Xu
  • How to search DTP/NCI Compounds An easier option is to use Enhanced NCI Database Browser 2.2 Query Data Value, paste SMILES string and set Tc threshold ...
    Posted Sep 5, 2016, 2:34 PM by Dong Xu
  • Python install pip, scipy, numpy, matplotlib Get pip first:Just follow the instructions here: Securely download sure the python version is in the current SEARCH PATH , run sudo python ...
    Posted Mar 1, 2016, 11:12 AM by Dong Xu
  • Adduser vs Useradd (Debian/Ubuntu) Should use adduser which is a perl script that calls useradd and has enhanced features: a ...
    Posted Sep 23, 2017, 3:03 PM by Dong Xu
  • Intel WiDi installation 1. download and run Intel® WiDi Compatibility Tool Get WiDi update tool ...
    Posted Feb 5, 2016, 11:12 AM by Dong Xu
  • Configure X11/Xorg gdm after switching monitors or video cards A potential universal solution is:1. backup the current /etc/X11/xorg.conf2. reinstall nvidia driver3. use xorg.conf.saxsave and replace Device Section as follows. Note that ...
    Posted Feb 3, 2016, 2:24 PM by Dong Xu
  • Linux OS Disk Clone and ext3 resize, fdisk change partition type Essentially, to resize (shrink or enlarge) ext3 partition, we have to use resize2fs. Other methods are unsafeAomei and ddrescue are preferred methods for cloning Linux disks, albeit slower. Aomei ...
    Posted Mar 30, 2016, 9:37 AM by Dong Xu
  • Disk Clone Tools Samsung SSD: use Samsung data migration softwareOther SSD/HD requiresGPT and UEFI, recovery partition supportChoice:Macrium Reflect  (free or non-free version)Paragon's Migrate to SSD ...
    Posted Jan 24, 2016, 12:07 AM by Dong Xu
  • Backup to ACD Amanzon Cloud Drive Use rclone, copy the entire drive D including sub-dirs to ACDrclone.exe -c --log-file=test.log -v copy D:/ remote:wasabi/dnohup rclone -c -v --no ...
    Posted Jan 14, 2016, 1:12 PM by Dong Xu
  • Port Forwarding to Virtual Machine VMWare Workstation users can select Edit –> Virtual Network Editor then follow ...
    Posted Jan 3, 2016, 7:20 PM by Dong Xu
  • Remote desktop from Linux rdesktop -g 1920x1080 host
    Posted Dec 31, 2015, 4:50 PM by Dong Xu
  • Denyhosts vs. iptables Note that DenyHosts will infact block other services - the main difference is that ...
    Posted Dec 30, 2015, 9:50 PM by Dong Xu
  • Setup Crontab/Rsync Automatic Backup on Windows The latest technology is to use WSL, crontab, and rsync: to add yourself to the ...
    Posted Oct 24, 2017, 2:39 PM by Dong Xu
  • GPU Performance Tweak, GPU Boost Warning: Tweaking GPU Boost may be more than its worth because setting higher mclk/pclk will increase GPU temp and stability, triggering auto-throttle and resulting in lower performance. We ...
    Posted Dec 28, 2015, 2:58 PM by Dong Xu
  • FFMPEG CUDA acclerated (using NVEC)
    Posted Dec 24, 2015, 2:30 PM by Dong Xu
  • Monitor CPU/GPU/Mem Utilization CPU/System Monitorvmstat -n 1GPU Monitor nvidia-smi dmon            Displays device stats in scrolling formatnvidia-smi pmon            Displays process stats in scrolling format.nvidia-smi topo -m ...
    Posted Dec 24, 2015, 2:26 PM by Dong Xu
  • Linux Kill Command Generally, you should use kill -15 before kill -9 to give the target process a chance to clean up after itself. (Processes can't catch or ignore SIGKILL, but they ...
    Posted Dec 24, 2015, 10:30 AM by Dong Xu
  • Select GPU for desmond MD jobs on a Multiple-CPU computer (compute and persistence mode) and set power limit Reference: a GPU in  runlevel 3 Most clusters operate at  runlevel 3 ...
    Posted Jan 1, 2016, 9:59 AM by Dong Xu
  • Compile OpenCL App - BUDE Reference: of all, CUDA library did not provide the needed cl ...
    Posted Dec 6, 2015, 9:22 PM by Dong Xu
  • Compile gcc-4.9.3, gcc-5.4.0 Follow this: ...
    Posted Jan 4, 2018, 12:58 PM by Dong Xu
  • Gromacs 5.1 Installation Works with gromacs-5.1 using gcc 4.4cmake-3.3.2 ../ -DCMAKE_INSTALL_PREFIX=/garlic/apps/gromacs-5.1/single  -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g ...
    Posted Oct 14, 2015, 12:21 AM by Dong Xu
  • Journal Letters and Communications Nature communications (Impact factor‎: ‎11.47 cost $5200, a bit too much)Nature Scientific Reports (IF: 5.578, cost ~$1500): ...
    Posted Sep 18, 2015, 3:31 PM by Dong Xu
  • JChem Excel Setup
    Posted Sep 16, 2015, 8:24 PM by Dong Xu
  • yast zypper pacman bad key fuse-exfat sudo zypper in -d fuse-exfat #This downloads the rpm file but does not install sudo rpm -i --force --nodeps --nosignature /var/cache/zypp/packages/Essentials/x86_64/fuse-exfat ...
    Posted Sep 7, 2015, 2:10 PM by Dong Xu
  • Move windows 8 user folder Open up ...
    Posted Sep 1, 2015, 12:23 PM by Dong Xu
  • Ginger: ECS LIVA Box to run Linux Runs Linux (two distributions) with no problems AFTER setting the UEFI to non-protected boot.
    Posted Aug 12, 2015, 9:45 PM by Dong Xu
  • ASUS BIOS Config for AMD FX-8350 FX-8350 Scientific performance: the following CPU config ...
    Posted Aug 12, 2015, 9:49 AM by Dong Xu
  • iptables, delete/unblock an IP address iptables -D INPUT -s  x.x.x.x -j DROPiptables -D INPUT -s  x.x.x.x/32 -j DROP ...
    Posted Jul 29, 2015, 5:53 PM by Dong Xu
  • Disable ubuntu nginx web server sudo service nginx stopTo disable autostart nginx servicesudo update-rc.d -f nginx disableapt-get remove nginxvs.apt-get purge nginxFirst one removes all package ...
    Posted Jul 28, 2015, 7:04 PM by Dong Xu
Showing posts 1 - 100 of 208. View more »

SAS and Python, SASPy, SAS_Kernel for Jupyter Notebook

posted Mar 27, 2018, 6:17 PM by Dong Xu   [ updated Mar 27, 2018, 6:23 PM ]

SAS Programming for R Users (Course Materials)

In SAS environments outside of SAS University Edition, here's what you need to run SAS with Jupyter:
  • SAS 9.4 or later running on Windows, Linux, or even z/OS (see support for SASPy, the underlying package)
  • Python 3 installed on the same machine (that's basically part of Linux)
  • Access to the OS shell to install/configure the Jupyter Notebook infrastructure and the sas_kernel.

Log compilation, installation steps

posted Feb 15, 2018, 9:27 AM by Dong Xu

./configure --prefix=/home/you/mpich-install  2>&1 | tee config.log  (bash)

|& tee (csh)

make VERBOSE=1 |& tee make.log (for csh and tcsh)
make VERBOSE=1 2>&1 | tee make.log   (for bash and sh)
VERBOSE=1 (optional)

make install |& tee makeinstall.log
make install 2>&1 | tee makeinstall.log

./configure \

\ means that this is really one line.

Linux hardware info

posted Feb 11, 2018, 5:07 PM by Dong Xu   [ updated Feb 14, 2018, 2:45 PM ]

M.2 drive SSD vs NVMe

posted Feb 7, 2018, 8:44 AM by Dong Xu   [ updated Feb 7, 2018, 11:13 AM ]

Are all M.2 drives NVMe?

No. Remember, M.2 is just the form factor. M.2 drives can come in SATA versions (like the Crucial MX300 M.2 for example) and NVMe versions (like the Samsung 960 Pro), which describes the bus they use to electrically communicate with the other PC components. SATA M.2 SSD drives and 2.5” SATA SSDs actually operate at virtually identical spec. NVMe M.2’s on the other hand, definitely do not, as we’re about to discuss.

How does NVMe speed compare to SATA?

Modern motherboards use SATA III which maxes out at a throughput of 600MB/s (or 300MB/s for SATA II, in which case, it’s time to upgrade). Via that connection, most SSDs will provide Read/Write speeds in the neighborhood of 530/500 MB/s. For comparison, a 7200 RPM SATA drive manages around 100MB/s depending on age, condition, and level of fragmentation. NVMe drives, on the other hand, provide write speeds as high as 3500MB/s. That’s 7x over SATA SSDs!

the newer USB 3.0, which can handle up to 5gbps (640MBps)

The 6Gbps SATA spec allows for up to 750MB/s of bandwidth, but the PCIe 2.0 x1 interface limits read/write speed to 500MB/s.

View and convert SVG file on Linux and Windows

posted Feb 6, 2018, 10:58 AM by Dong Xu

On SUSE, install rsvg-view from yast2

Viewer:  rsvg-view-3 filename.svg

Converter:  -f, --format=[png, pdf, ps, eps, svg, xml, recording]

rsvg-convert C2-C1-C3-C6.svg -o C2-C1-C3-C6.png

Inkscape can be used on both Linux and Windows

tar to stdout

posted Jan 10, 2018, 9:07 PM by Dong Xu

tar xvf archive.tar -O | less
tar xvf archive.tar -O | grep [ ]

For a file inside tar file

tar xvf archive.tar file_with_path -O | less
tar xvf archive.tar file_with_path -O | grep [ ]

CXX11 compilation error

posted Jan 6, 2018, 10:00 AM by Dong Xu

If you get linker errors about undefined references to symbols that involve types in the std::__cxx11 namespace or the tag [abi:cxx11] then it probably indicates that you are trying to link together object files that were compiled with different values for the _GLIBCXX_USE_CXX11_ABI macro. This commonly happens when linking to a third-party library that was compiled with an older version of GCC. If the third-party library cannot be rebuilt with the new ABI then you will need to recompile your code with the old ABI.

Not all uses of the new ABI will cause changes in symbol names, for example a class with a std::string member variable will have the same mangled name whether compiled with the old or new ABI. In order to detect such problems the new types and functions are annotated with the abi_tag attribute, allowing the compiler to warn about potential ABI incompatibilities in code using them. Those warnings can be enabled with the -Wabi-tag option.

Amber16 + AmberTool17 installation

posted Dec 30, 2017, 10:07 AM by Dong Xu   [ updated Feb 15, 2018, 3:46 PM ]

sudo conda create -n amber16 python=2.7
install the following packages:

sudo yast2
install  libbz2-1 libbz2-devel

export AMBERHOME=/garlic/apps/Downloads/Amber16/amber16/
sudo cp -s /usr/bin/gfortran-4.8 /usr/bin/gfortran
./configure --full-help

sudo CUDA_HOME=/garlic/apps/cuda8.0 ./configure -cuda -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
test -f $
sudo CUDA_HOME=/garlic/apps/cuda8.0 make install

sudo ./configure -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
test -f $
sudo make install

sudo PATH=/garlic/apps/mpich3.1.4/bin:$PATH ./configure -mpi -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
PATH=/garlic/apps/mpich-3.2.1_gnu/bin:$PATH ./configure -mpi -noX11 --skip-python gnu 2>&1 | tee config.log

test -f $AMBERHOME/
source $AMBERHOME/
sudo PATH=/garlic/apps/mpich3.1.4/bin:$PATH make install

For Amber14+AmberTools15:
export AMBERHOME=/garlic/apps/Downloads/Amber14/amber14/
cp -rv pmemd/* /garlic/apps/Downloads/Amber14/amber14/src/pmemd/

MDL Mol/SDF V2000 vs V3000

posted Dec 24, 2017, 3:29 PM by Dong Xu   [ updated Dec 24, 2017, 3:31 PM ]

Most apps: obabel, ChemAxon etc. can handle the conversion:

1000-atom limit


GSMACCS-II07189510252D 1   0.00366     0.00000     0
Example taken from Symyx CTFile formats (pdf) p.83 Nov.07
  0  0  0     0  0            999 V3000
M  V30 COUNTS 6 5 0 0 1
M  V30 1 C -0.6622 0.5342 0 0 CFG=2
M  V30 2 C 0.6622 -0.3 0 0
M  V30 3 C -0.7207 2.0817 0 0 MASS=13
M  V30 4 N -1.8622 -0.3695 0 0 
M  V30 5 O 0.622 -1.8037 0 0
M  V30 6 O 1.9464 0.4244 0 0 
M  V30 1 1 1 2
M  V30 2 1 1 3 CFG=1
M  V30 3 1 1 4
M  V30 4 2 2 5
M  V30 5 1 2 6

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