736f5d2177478711329481540416232cf9a4202a
old/Home.md
| ... | ... | @@ -1,28 +0,0 @@ |
| 1 | - |
|
| 2 | -# OLD |
|
| 3 | -These pages are old and out-of-date. They're kept as some of this legacy information may be helpful. |
|
| 4 | - |
|
| 5 | - |
|
| 6 | -# Lab Support |
|
| 7 | - |
|
| 8 | -Support Information for SBGrid Core Supported Labs: |
|
| 9 | - |
|
| 10 | -* [Bradner Lab DFCI](howto-bradner-lab-dfci) |
|
| 11 | -* [D'Souza Lab Harvard University](howto-d-souza-lab-harvard-university) |
|
| 12 | -* Shared Resources for Labs at [Longwood Center labs DFCI](howto-eck-lab-dfci) including: |
|
| 13 | - * Dhe-Paganon Lab |
|
| 14 | - * Eck Lab |
|
| 15 | - * Fischer Lab |
|
| 16 | - * Wang Lab |
|
| 17 | - |
|
| 18 | -* [Gaudet Lab Harvard University](./howto-gaudet-lab-harvard-university) |
|
| 19 | -* [Heldwein Lab Tufts Univertsity](./howto-heldwein-lab-tufts) |
|
| 20 | -* [Kahne Lab Harvard University](./howto-kahne-lab-harvard-university) |
|
| 21 | -* [kirchhausen Lab, BCH](./howto-kirchhausen-lab-bch) |
|
| 22 | -* [Leschziner Lab Harvard University](./howto-leschziner-lab-harvard-university) |
|
| 23 | -* [Miller Lab MGH](./howto-miller-lab-mgh) |
|
| 24 | -* [Sliz Lab Harvard Medical School](./howto-sliz-lab) |
|
| 25 | -* [Springer Lab BCH](./howto-springer-lab-bch) |
|
| 26 | -* [Dhe-Paganon Lab](./howto-structural-biol-core-dhe-paganon-lab-dfci) |
|
| 27 | -* [Wei Lab Genzyme](./howto-wei-lab) |
|
| 28 | -* [Wucherpfennig Lab DFCI](./howto-wucherpfennig-lab-dfci) |
|
| ... | ... | \ No newline at end of file |
old/README.md
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| 1 | -These files are for historical purposes and verisons of the content we |
|
| 2 | -had on our old forums at forums.sbgrid.org. |
|
| ... | ... | \ No newline at end of file |
old/_Sidebar.md
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| 1 | - **[Core Wiki](../Home)** |
|
| 2 | - |
|
| 3 | -##### Help |
|
| 4 | -* [How To Get Help & Support](../faq-getting-help) |
|
| 5 | -* [Lab Support](../Home) |
|
| 6 | -* [FAQ](../faqs) |
old/howto-bradner-lab-dfci.md
| ... | ... | @@ -1,50 +0,0 @@ |
| 1 | -# HOWTO, Bradner Lab, DFCI |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -#Site Overview: |
|
| 4 | -Members of the Bradner Lab at the Dana Farber Cancer Institute have access to |
|
| 5 | -a Linux workstation in the wet lab, running a large collection of structural |
|
| 6 | -biology software. It shares authentication and data directories and can be |
|
| 7 | -only accessed locally from within the lab. |
|
| 8 | - |
|
| 9 | -Research Computing support is provided by SBGrid. Pl ease contact SBGrid |
|
| 10 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 11 | - |
|
| 12 | -## Workstations: |
|
| 13 | - |
|
| 14 | -Name|OS|Hardware Configuration|Location|Notes |
|
| 15 | ----|---|---|---|--- |
|
| 16 | -jbl1|Sci Linux 5|Intel Core i7 at 3.20GHz. 4 cores. 6GB of RAM. Nvidia Quadro 600.| |Last checked: 11/17/2014 |
|
| 17 | - |
|
| 18 | -##Data Backups: |
|
| 19 | - |
|
| 20 | -Backups on the linux workstations are performed on a regular basis by the |
|
| 21 | -research computing group at DFCI. If you have any questions about backups, |
|
| 22 | -need files restored, or have any general issue regarding backups, contact the |
|
| 23 | -Research Computing group via this web page: [Help Me - DFCI Reseach |
|
| 24 | -Computing](http://research4.dfci.harvard.edu/content/helpme) . |
|
| 25 | - |
|
| 26 | -## X-Ray Data Collection: |
|
| 27 | - |
|
| 28 | -Plum and Aqua are workstations designated for data collection, and are located |
|
| 29 | -in the X-Ray room. These machines have custom local software installs to |
|
| 30 | -interact with the Marresearch scanner. |
|
| 31 | - |
|
| 32 | -HKL2000 can be accessed and run on Plum, Aqua, and MJEL12. |
|
| 33 | - |
|
| 34 | -Please contact Mike Eck to obtain guest privileges. |
|
| 35 | - |
|
| 36 | -## Networking and General IT Support: |
|
| 37 | - |
|
| 38 | -To report problems regarding the network at DFCI, or general computing |
|
| 39 | -support, contact the Partners Healthcare Help desk at: |
|
| 40 | -[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only |
|
| 41 | -works from a Partners network connection) |
|
| 42 | - |
|
| 43 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 44 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 45 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 46 | - |
|
| 47 | - |
|
| 48 | - |
|
| 49 | - |
|
| 50 | - |
old/howto-d-souza-lab-harvard-university.md
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| 1 | -# HOWTO, D'Souza Lab, Harvard University |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | -Members of the D’Souza Lab at Harvard University have access to five Linux |
|
| 5 | -workstations running a large collection of structural biology software. These |
|
| 6 | -workstations share authentication and data directories. |
|
| 7 | - |
|
| 8 | -Research Computing support is provided by SBGrid. P lease contact SBGrid |
|
| 9 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 10 | - |
|
| 11 | -##Workstations: |
|
| 12 | - |
|
| 13 | - |
|
| 14 | -| Name | Operating System | Hardware Configuration|Location|Notes| |
|
| 15 | -|---|---|---|---|---| |
|
| 16 | -|chef|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014| |
|
| 17 | -|clyde|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro 4000|NW 311|09/25/2014| |
|
| 18 | -|jack|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GH. 4 Cores. 16G of RAM. Nvidia GeForce 9600GT. |NW 311 |09/25/2014| |
|
| 19 | -|kenny|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro FX 380.| NW 311 |09/25/2014 |
|
| 20 | -|rufus|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014|HKL2000 licensed system. |
|
| 21 | - |
|
| 22 | -##Printers: |
|
| 23 | - |
|
| 24 | -| Name | Model | Location | Notes | |
|
| 25 | -|---|---|---|---| |
|
| 26 | -|carmen|HP LaserJet 4700|Computer Lab|color printer| |
|
| 27 | -|vger|Ricoh Aficio C410|Wet Lab|color printer |
|
| 28 | - |
|
| 29 | -## Data Replication: |
|
| 30 | - |
|
| 31 | -Data is replicated to a secondary server. Snapshots are taken every hour and |
|
| 32 | -kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up |
|
| 33 | -to 12 months. If you need a file restored, please contact SBGrid |
|
| 34 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 35 | - |
|
| 36 | -## Remote access: |
|
| 37 | - |
|
| 38 | -SSH access is available through galactica.mcb.harvard.edu . Remote access is |
|
| 39 | -not enabled by default. If you need to access Galactica remotely, please |
|
| 40 | -contact SBGrid [here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 41 | - |
|
| 42 | -##Networking and General IT Support: |
|
| 43 | - |
|
| 44 | -To report problems regarding the network at Harvard University, or general |
|
| 45 | -computing support, contact the Harvard University Help desk. |
|
| 46 | - |
|
| 47 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 48 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 49 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 50 | - |
|
| 51 | - |
|
| 52 | - |
old/howto-eck-lab-dfci.md
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| 1 | -# HOWTO, Longwood Center labs, DFCI |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | - |
|
| 5 | -### |
|
| 6 | - |
|
| 7 | -* Eck |
|
| 8 | -* Dhe-Paganon |
|
| 9 | -* Wang |
|
| 10 | -* Fischer |
|
| 11 | - |
|
| 12 | - |
|
| 13 | -Members of these labs at the Dana Farber Cancer Institute have access to |
|
| 14 | -several shared Linux and Mac computers running a large collection of |
|
| 15 | -structural biology software. The Linux computers share authentication and data |
|
| 16 | -directories and can be only accessed locally from within the lab. |
|
| 17 | - |
|
| 18 | -Linux computers are located in the graphics room (fish bowl) on the third |
|
| 19 | -floor and in cubicles on the fourth floor. The X-ray room has two workstations |
|
| 20 | -for data acquisition. Macs are located on lab member’s desks. |
|
| 21 | - |
|
| 22 | -All linux machines are configured for Stereo 3D output. |
|
| 23 | - |
|
| 24 | -Research Computing support is provided by SBGrid - contact them |
|
| 25 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 26 | - |
|
| 27 | - |
|
| 28 | -## Shared Workstations: (see below) |
|
| 29 | - |
|
| 30 | - |
|
| 31 | - |
|
| 32 | -## Mac Workstations: (see below) |
|
| 33 | - |
|
| 34 | - |
|
| 35 | - |
|
| 36 | -## Home and Data Directories: |
|
| 37 | - |
|
| 38 | -### Linux systems: |
|
| 39 | - |
|
| 40 | -NFS mounted home directories: **/nfs/<PI initials>/<username>** |
|
| 41 | - |
|
| 42 | -NFS mounted synchrotron data:** /synchrotron** |
|
| 43 | - |
|
| 44 | -NFS read only mounted programs tree: **/programs** |
|
| 45 | - |
|
| 46 | - |
|
| 47 | - |
|
| 48 | -### On Mac systems: |
|
| 49 | - |
|
| 50 | -NFS read only mounted home directories: **/nfs/<PI |
|
| 51 | -initials>/<username>** |
|
| 52 | - |
|
| 53 | -NFS read only mounted synchrotron data: **/synchrotron** |
|
| 54 | - |
|
| 55 | -NFS read only mounted programs tree: **/programs** |
|
| 56 | - |
|
| 57 | -SMB read and write mounted home directory: |
|
| 58 | - |
|
| 59 | -To mount your home directory using Samba (SMB): |
|
| 60 | - |
|
| 61 | -\- In Finder, click **Go** then click **'Go to Server'** |
|
| 62 | - |
|
| 63 | -\- Type in server address: **smb://blacker.in.hwlab** |
|
| 64 | - |
|
| 65 | -\- Enter your SMB username and password. (contact SBGrid for SMB account |
|
| 66 | -issues) |
|
| 67 | - |
|
| 68 | -To change your SMB password, use this command on a **linux** system: |
|
| 69 | - |
|
| 70 | - 1. smbpasswd -R blacker.in.hwlab -U <username> |
|
| 71 | - |
|
| 72 | - |
|
| 73 | - |
|
| 74 | -## Data Backups: |
|
| 75 | - |
|
| 76 | -Fileserver data is snapshotted and also replicated to another server at HMS/C |
|
| 77 | -building. Local iMac accounts are backed up using crashplan. |
|
| 78 | - |
|
| 79 | -## Printing: |
|
| 80 | - |
|
| 81 | -A Xerox Phaser 8860 is located in the third floor near the kitchen area. |
|
| 82 | -Another inkJet printer is located directly above on the fourth floor. If you |
|
| 83 | -are having issues with printing, please contact SBGrid |
|
| 84 | -[here](https://sbgrid.org/help/?tab=contact-us). |
|
| 85 | - |
|
| 86 | -## X-Ray Data Collection: |
|
| 87 | - |
|
| 88 | -Plum and Aqua are workstations designated for data collection, and are located |
|
| 89 | -in the X-Ray room on the third floor. These machines have custom local |
|
| 90 | -software installs to interact with the Marresearch scanner. |
|
| 91 | - |
|
| 92 | -HKL2000 can be accessed and run on Plum, Aqua, mjel14 and sdp2. |
|
| 93 | - |
|
| 94 | -Please contact Mike Eck to obtain guest privileges. |
|
| 95 | - |
|
| 96 | -## Remote Access: |
|
| 97 | - |
|
| 98 | -External SSH access is available at crystal.harvard.edu. |
|
| 99 | - |
|
| 100 | -**Forwarding your red email to Crystal:** |
|
| 101 | - |
|
| 102 | -* Please contact SBGrid help if you have questions about forwarding. |
|
| 103 | - |
|
| 104 | -## Networking and General IT Support: |
|
| 105 | - |
|
| 106 | -To report problems regarding the network at DFCI, or general computing |
|
| 107 | -support, contact the Partners Healthcare Help desk at: |
|
| 108 | -[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only |
|
| 109 | -works from a Partners network connection) |
|
| 110 | - |
|
| 111 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 112 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 113 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 114 | - |
|
| 115 | -## Shared Linux Workstations: |
|
| 116 | - |
|
| 117 | -| Name | OS | Hardware Configuration|Location|Notes| |
|
| 118 | -|---|---|---|---|---| |
|
| 119 | -|aqua|Sci Linux 6|Intel Core 2 Duo at 3.33GHz. 2 cores. 1GB or RAM. Nvidia Quadro FX 3700.|X-Ray room(Longwood Center) |Last checked: 13/09/2015, HKL2000 licensed, Works with Marresearch scanner | |
|
| 120 | -|plum|Sci Linux 6 |AMD Athlon 64 Dual Core Processor 4800+. 2 cores. 1GB of RAM.|X-Ray room (Longwood Center)|Last checked: 03/09/2015, HKL2000 licensed, Works with Marresearch scanner | |
|
| 121 | -|mjel11|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015| |
|
| 122 | -|mjel12|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015, HKL2000 licensed| |
|
| 123 | -|mjel13|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM.| Wet lab|Last checked: 03/03/2015| |
|
| 124 | -|mjel14|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 32 GB of RAM. Nvidia Quadro 4000.| Graphics room ((Longwood Center)|Last checked: 03/09/2015 \ |
|
| 125 | -|mjel15|Sci Linux 6|Intel Core i7 at 3.60GHz. 4 cores. 16 GB of RAM. Nvidia Quadro 4000.| Computer lab|Last checked: 03/04/2015 \ |
|
| 126 | -|xrc1|Sci Linux 6|Intel Core Quad at 2.66GHz. 4 cores. 4GB of RAM. Nvidia Quadro FX 1400| Graphics room (Longwood Center)|Last checked: 03/02/2015 \ |
|
| 127 | - |
|
| 128 | -## Mac Workstations: |
|
| 129 | - |
|
| 130 | -| Name | OS | Hardware Configuration|Account Backed up| Administrator | |
|
| 131 | -|---|---|---|---|---| |
|
| 132 | -|wood-imac|OSX 10.10.5|iMac10,1, Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes|David Wood | |
|
| 133 | -|mje-dwood-imac|OSX 10.5.8|iMac8,1, Intel Core 2 Duo 2.66 GHz 2 Cores, Memory: 2 GB, ATI Radeon HD 2600 Pro, |No| |
|
| 134 | -|jwh-macpro|OSX 10.8.5|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 10 GB, NVIDIA Quadro FX 5600, |Yes|Jia-Huai | |
|
| 135 | -|yiquns-imac|OSX 10.8.5|iMac11,2, Intel Core i3 3.06 GHz 2 Cores Memory: 4 GB ATI Radeon HD 4670|Yes|SBGrid, (user: hjeon) | |
|
| 136 | -|randalls-imac (broken)|OSX 10.8.5|iMac10,1 Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes| Randall McNally | |
|
| 137 | -|mike_eck_macpro|OSX 10.9.4|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 8GB, NVIDIA Quadro FX 5600|Yes|Mike Eck | |
|
| 138 | -|humayuns-imac|OSX 10.10.1|iMac14,2 Intel Core i5 4 Cores, Memory 16GB, NVIDIA GeForce GT 755M| Yes|Humayun Sharif | |
|
| 139 | -|asher-page-imac|OSX 10.8.5|iMac13,1 Intel Core i5 2.7 GHz 4 Cores, Memory: 8GB,NVIDIA GeForce GT 640M|Yes|Randall McNally | |
|
| 140 | -|li-imac|tbd|tbd|Yes|Qing Li | |
|
| 141 | -|dhcp-155-52-53-43|tbd|tbd| |common iMac (gel reader)| |
|
| 142 | - |
|
| 143 | - |
|
| 144 | - |
old/howto-gaudet-lab-harvard-university.md
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| 1 | -# HOWTO, Gaudet Lab, Harvard University |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | -Members of the Gaudet Lab at Harvard University have access to two graphical |
|
| 5 | -workstations , Pioneer and Cobincho, and a regular workstation ‘Curry’, all |
|
| 6 | -running a large collection of structural biology software. The linux |
|
| 7 | -workstations share authentication and data directories. Pioneer contains a |
|
| 8 | -license for running HKL2000. |
|
| 9 | - |
|
| 10 | -Research Computing support is provided by SBGrid. P lease contact SBGrid |
|
| 11 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 12 | - |
|
| 13 | -## Workstations: |
|
| 14 | - |
|
| 15 | -|Name|Operating System|Hardware Configuration|Location|Last Checked|Notes| |
|
| 16 | -|---|---|---|---|---|--- |
|
| 17 | -|cobincho|CentOS 6.5, |Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014 |
|
| 18 | -| curry|CentOS 6.5|Intel Core i7 CPU at 2.8GHz, 4 Cores. 2GB of RAM. Nvidia Quadro FX 380. |NW 305|10/27/2014 |
|
| 19 | -| pioneer|CentOS 6.4|Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014|HKL2000 licensed system. |
|
| 20 | - |
|
| 21 | -## Printers: |
|
| 22 | - |
|
| 23 | -|Name|Model|Location|Notes| |
|
| 24 | -|---|---|---|--- | |
|
| 25 | -|carmen|HP LaserJet 4700|Computer Lab|color printer |
|
| 26 | -|vger|Ricoh Aficio C410|Wet Lab|color printer |
|
| 27 | - |
|
| 28 | -## Using SBGrid programs: |
|
| 29 | - |
|
| 30 | -All applications are located in ```/programs``` directory and are configured to run without additional settings. In most cases, you will easily be able to run any |
|
| 31 | -program in the collection by opening up a terminal shell, and typing the name |
|
| 32 | -of the program that you want to run. |
|
| 33 | - |
|
| 34 | -## Data Replication: |
|
| 35 | - |
|
| 36 | -Data is replicated to a secondary server. Snapshots are taken every hour and |
|
| 37 | -kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up |
|
| 38 | -to 12 months. If you need a file restored, please contact SBGrid |
|
| 39 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 40 | - |
|
| 41 | -##Remote access: |
|
| 42 | - |
|
| 43 | -SSH access is available through galactica.mcb.harvard.edu . Remote access is |
|
| 44 | -not enabled by default. If you need to access Galactica remotely, please |
|
| 45 | -contact SBGrid [here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 46 | - |
|
| 47 | -##Networking and General IT Support: |
|
| 48 | - |
|
| 49 | -To report problems regarding the network at Harvard University, or general |
|
| 50 | -computing support, contact the Harvard University Help desk. |
|
| 51 | - |
|
| 52 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 53 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 54 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
old/howto-heldwein-lab-tufts.md
| ... | ... | @@ -1,45 +0,0 @@ |
| 1 | -# HOWTO, Heldwein Lab, Tufts |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | -Members of the Heldwein lab at Tufts University have access to three Linux |
|
| 5 | -computers and a Mac workstation running a large collection of structural |
|
| 6 | -biology software. The Linux computers share authentication and data |
|
| 7 | -directories and can be only accessed locally from within the lab. Lab members |
|
| 8 | -also have access to an HP LaserJet printer. Research Computing support is |
|
| 9 | -provided by SBGrid. Please contact SBGrid |
|
| 10 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 11 | - |
|
| 12 | -## WOrkstations |
|
| 13 | - |
|
| 14 | -Name|OS|Hardware Configuration|Location|Notes |
|
| 15 | ----|---|---|---|--- |
|
| 16 | -ruby|Sci Linux 6.5| Intel Core i7 at 3.20GHz. 6 cores. 16GB of RAM. Nvidia Quadro 400| |Last checked: 11/13/2014 |
|
| 17 | -diamond|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014 |
|
| 18 | -beryl|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014 |
|
| 19 | - |
|
| 20 | -## Storage and Backup: |
|
| 21 | - |
|
| 22 | -Backup of /nfs/home, which is hosted via Tufts NAS, are performed by the IT |
|
| 23 | -group at Tufts University. |
|
| 24 | - |
|
| 25 | -## Using SBGrid programs: |
|
| 26 | - |
|
| 27 | -All applications are located in /programs directory and are configured to run |
|
| 28 | -without additional settings. |
|
| 29 | - |
|
| 30 | -Most of the software titles installed in the SBGrid Suite have several |
|
| 31 | -versions available. Typically, we try to provide at least three versions of |
|
| 32 | -each software package, although very old or very new applications may have |
|
| 33 | -fewer versions. To override the default version, follow these instructions. |
|
| 34 | - |
|
| 35 | -Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid- |
|
| 36 | -programs) if you need information on how to run SBGrid programs remotely or |
|
| 37 | -locally on your machine. |
|
| 38 | - |
|
| 39 | -## General IT Support: |
|
| 40 | - |
|
| 41 | -Support for office computing is provided by Tufts IT. |
|
| 42 | - |
|
| 43 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 44 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 45 | - |
old/howto-kahne-lab-harvard-university.md
| ... | ... | @@ -1,35 +0,0 @@ |
| 1 | -# HOWTO, Kahne Lab, Harvard University |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -# Site Overview: |
|
| 4 | -Members of the Kahne Lab at Harvard University have access to Linux and Mac |
|
| 5 | -workstations running a large collection of structural biology software. |
|
| 6 | - |
|
| 7 | -Research Computing support is provided by SBGrid. P lease contact SBGrid |
|
| 8 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 9 | - |
|
| 10 | -## Workstations: |
|
| 11 | - |
|
| 12 | -Name|OS|Hardware Configuration|Location|Notes| |
|
| 13 | ----|---|---|---|---| |
|
| 14 | -blain|Sci Linux, 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM.Nvida GeForce GTX 760. || Last checked: 11/03/2014 |
|
| 15 | -billy|OS X 10.6.8, |Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770. | |Last checked: 10/27/2014. HKL2000 licensed machine. |
|
| 16 | -dutch|Sci Linux 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM. Nvida GeForce GTX 760.| |Last checked: 10/27/2014 |
|
| 17 | -mac|OS X 10.6.8|Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770.| |Last checked: 10/27/2014 |
|
| 18 | - |
|
| 19 | -## Data Backups: |
|
| 20 | - |
|
| 21 | -TBD |
|
| 22 | - |
|
| 23 | -## Networking and General IT Support: |
|
| 24 | - |
|
| 25 | -To report problems regarding the network at Harvard University, or general |
|
| 26 | -computing support, contact the Harvard University Help desk. |
|
| 27 | - |
|
| 28 | -## Remote access: |
|
| 29 | - |
|
| 30 | -SSH access is available through 128.103.94.191. This accesses the primary |
|
| 31 | -Linux workstation. |
|
| 32 | - |
|
| 33 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 34 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 35 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
old/howto-kirchhausen-lab-bch.md
| ... | ... | @@ -1,70 +0,0 @@ |
| 1 | -# HOWTO, Kirchhausen Lab, BCH |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | - |
|
| 4 | -## Site Overview: |
|
| 5 | -Members of the Kirchhausen Lab at the Children’s Hospital Boston have access |
|
| 6 | -to a large collection of structural biology software. Research Computing |
|
| 7 | -support is provided by SBGrid. Please contact them [here |
|
| 8 | -](https://sbgrid.org/help/?tab=contact-us) . |
|
| 9 | - |
|
| 10 | -# Data Backups: |
|
| 11 | - |
|
| 12 | -Full and incremental backups of SBGrid file servers are conducted. This |
|
| 13 | -includes your home and data directories. In general, backups are kept for |
|
| 14 | -three months, and then are stored on physical media for archival purposes. If |
|
| 15 | -you need a file restored, please contact SBGrid [here |
|
| 16 | -](https://sbgrid.org/help/?tab=contact-us) . |
|
| 17 | - |
|
| 18 | -## Networking and General IT Support: |
|
| 19 | - |
|
| 20 | -Contact Children’s help desk at (617) 919 4357 or at [ |
|
| 21 | -](mailto:help.desk@childrens.harvard.edu) [ |
|
| 22 | -](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu) |
|
| 23 | -. |
|
| 24 | - |
|
| 25 | -* [ Using SBGrid programs ](http://forums.sbgrid.org/topic/using-sbgrid- |
|
| 26 | -programs) |
|
| 27 | -*[ Getting help from SBGrid ](http://forums.sbgrid.org/topic/getting-help) |
|
| 28 | -*[ Other Resources ](http://forums.sbgrid.org/topic/other-resources) |
|
| 29 | - |
|
| 30 | - |
|
| 31 | -##Synchronizing working directories between tklab and orchestra** |
|
| 32 | - |
|
| 33 | -### Overview |
|
| 34 | - |
|
| 35 | -The [ data synchronization ](http://forums.sbgrid.org/topic/tklab-data- |
|
| 36 | -synchronization-to-orchestra) process is a one-way synchronization, and files |
|
| 37 | -and directories transfered are no longer writable. For processing, there is a |
|
| 38 | -two-way synchronization of the ` ~/sync ` directory between the ` tklab ` |
|
| 39 | -server and ` orchestra ` . Since the ` ~/sync ` directories are in the user's |
|
| 40 | -home directories, users have full ability to create, delete, rename, etc |
|
| 41 | -anything within them without effecting the raw images stored in ` |
|
| 42 | -/groups/kirchhausen/datasync ` . |
|
| 43 | - |
|
| 44 | -**Anything outside the ` ~/sync ` directory, including ` .cshrc ` , ` .ssh ` will not be copied to orchestra.** |
|
| 45 | - |
|
| 46 | -### Suggested Working Directory Structure |
|
| 47 | - |
|
| 48 | -Symlinks can be used to keep the processing directories linked to the raw data |
|
| 49 | -directories, without requiring write/delete permissions for data directories. |
|
| 50 | -For example, instead of nstead of creating ` /datasync/Dataset001/process1 ` , |
|
| 51 | -create a ` ~/sync/Dataset001 ` directory. Within ` ~/sync/Dataset001 ` , |
|
| 52 | -create a symlink pointing to the images ( ` cd ~/sync/Dataset001 ; ln -s |
|
| 53 | -/groups/kirchhausen/datasync/Dataset001 images ` ). |
|
| 54 | - |
|
| 55 | -### Step by Step |
|
| 56 | - |
|
| 57 | -Setup [ passwordless ssh logins ](http://forums.sbgrid.org/topic/setting-up- |
|
| 58 | -passwordless-ssh) between ` tklab ` and ` orchestra ` before using two-way |
|
| 59 | -sync. |
|
| 60 | - |
|
| 61 | - 1. Process within the ` ~/sync ` directory, on ` orchestra ` or ` tklab ` . |
|
| 62 | - 2. When done, or at a checkpoint, initiate synchronization from ` tklab ` : ` unison -auto ` (interactive) or ` unison -batch ` (non-interactive). |
|
| 63 | - |
|
| 64 | -### More details |
|
| 65 | - |
|
| 66 | -Nightly non-interactive synchronization runs will be run from cron. |
|
| 67 | - |
|
| 68 | -If you're curious about unison, more detail is available from the [ project |
|
| 69 | -website ](http://www.cis.upenn.edu/~bcpierce/unison/download.html) . |
|
| 70 | - |
old/howto-leschziner-lab-harvard-university.md
| ... | ... | @@ -1,68 +0,0 @@ |
| 1 | -# HOWTO, Leschziner Lab, Harvard University |
|
| 2 | -Lab Moved and is no longer at HU. |
|
| 3 | - |
|
| 4 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 5 | - |
|
| 6 | -## Site Overview |
|
| 7 | -Members of the Leschziner Lab at Harvard University have access to 10 Linux |
|
| 8 | -and 2 Mac workstations running a large collection of structural biology |
|
| 9 | -software. The linux workstations share authentication and data directories and |
|
| 10 | -can be only accessed locally from within the computer room. |
|
| 11 | - |
|
| 12 | -Research Computing support is provided by SBGrid - contact them |
|
| 13 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 14 | - |
|
| 15 | - |
|
| 16 | -## Workstation** (see comment below) |
|
| 17 | -##Printers** (see comment below) |
|
| 18 | - |
|
| 19 | - |
|
| 20 | - |
|
| 21 | -## Data Replication |
|
| 22 | - |
|
| 23 | -Data is replicated to a secondary server. Snapshots are taken every hour and |
|
| 24 | -kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up |
|
| 25 | -to 12 months. If you need a file restored, please contact SBGrid |
|
| 26 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 27 | - |
|
| 28 | -##Remote access: |
|
| 29 | - |
|
| 30 | -SSH access is available through galactica.mcb.harvard.edu . Remote access is |
|
| 31 | -not enabled by default. If you need to access Galactica remotely, please |
|
| 32 | -contact SBGrid [here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 33 | - |
|
| 34 | -##Networking and General IT Support: |
|
| 35 | - |
|
| 36 | -To report problems regarding the network at Harvard University, or general |
|
| 37 | -computing support, contact the Harvard University Help desk. |
|
| 38 | - |
|
| 39 | - |
|
| 40 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 41 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 42 | -*[Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 43 | - |
|
| 44 | - |
|
| 45 | -## Workstations: |
|
| 46 | - |
|
| 47 | -Name|Operating System|Hardware Configuration|Location|Notes |
|
| 48 | ----|---|---|---|--- |
|
| 49 | -aida|Sci Linux, 6.5|Intel Core i7 CPU at 3.07GHz, 4 cores. 12GB of RAM. Nvidia Quadro 4000.|NW 305|Last checked 10/20/2014 |
|
| 50 | -dutchman|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz, 4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW311|Last checked 10/20/2014 |
|
| 51 | -fidelio|OSX, 10.6.4|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW305|Last checked 10/20/2014 |
|
| 52 | -figaro|OSX, 10.7.5|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW 305|Last checked 10/20/2014 |
|
| 53 | -giovanni|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014 |
|
| 54 | -isolde|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM.Nvidia NVS 290.|NW305|Last checked 10/20/2014 |
|
| 55 | -leginon|tbd|tbd|tbd| |
|
| 56 | -leonora|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014 |
|
| 57 | -otello|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz,4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW 305|Last checked 10/20/2014 |
|
| 58 | -tristan|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014 |
|
| 59 | -lothario|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz.6 cores. 32GB of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014 |
|
| 60 | -mignon|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz. 6 cores. 32G of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014 |
|
| 61 | - |
|
| 62 | -## Printers: |
|
| 63 | - |
|
| 64 | -Name|Model|Location|Notes |
|
| 65 | ----|---|---|--- |
|
| 66 | -carmen|HP LaserJet 4700|Computer Lab|color printer |
|
| 67 | -vger|Ricoh Aficio C410|Wet Lab|color printer |
|
| 68 | - |
old/howto-miller-lab-mgh.md
| ... | ... | @@ -1,22 +0,0 @@ |
| 1 | -# HOWTO, Miller Lab, MGH |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | -Members of the Miller Lab at MGH have remote access to the SBGrid software |
|
| 5 | -tree and can run jobs on Zorin. |
|
| 6 | - |
|
| 7 | -Research Computing support is provided by SBGrid. Pl ease contact SBGrid |
|
| 8 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 9 | - |
|
| 10 | -## Networking and General IT Support: |
|
| 11 | - |
|
| 12 | -To report problems regarding the network at MGH, or general computing support, contact the Partners Healthcare Help desk at: |
|
| 13 | -[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only |
|
| 14 | -works from a Partners network connection) |
|
| 15 | - |
|
| 16 | - |
|
| 17 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 18 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 19 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 20 | - |
|
| 21 | - |
|
| 22 | - |
old/howto-sliz-lab.md
| ... | ... | @@ -1,94 +0,0 @@ |
| 1 | -# HOWTO, Sliz Lab |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | - |
|
| 4 | -## Computing Accounts: |
|
| 5 | - |
|
| 6 | -Members of Sliz lab will generally have six computing accounts: |
|
| 7 | - |
|
| 8 | - * an HKL account for email, calendar and shared documents |
|
| 9 | - * a local (administrator) account for Mac OS X workstations |
|
| 10 | - * a CMCD account for login to the Linux workstation, to crystal.harvard.edu and to other Linux workstations at HMS. |
|
| 11 | - * an HMS account for login to eCommons and to HMS email system. |
|
| 12 | - * SBGrid account (optional) for software update. |
|
| 13 | - * DropBox account - this is a business account with unlimited backups and unlimited storage space. |
|
| 14 | - |
|
| 15 | -##Network: |
|
| 16 | -All computers in the lab should be connected to the SBGrid network. |
|
| 17 | -For connecting a personal computer, you will need to email the [MAC |
|
| 18 | -address](http://forums.sbgrid.org/topic/how-to-find-mac-address-on-os-x-gui) |
|
| 19 | -of the ethernet card or adaptor to [help@sbgrid.org](mailto:help@sbgrid.org) |
|
| 20 | -. In order to access SBGrid wi-fi network you will need to email your MAC |
|
| 21 | -address to [help@sbgrid.org](mailto:help@sbgrid.org) and request activation |
|
| 22 | -on the SBGrid wifi network; to connect, authenticate with your CMCD username |
|
| 23 | -and password. |
|
| 24 | - |
|
| 25 | - |
|
| 26 | - |
|
| 27 | -##Printing: |
|
| 28 | -We have two printers in the lab, which are both available from the |
|
| 29 | -SBGrid network. ps-laserjet3000dn is located in the wet lab area, ps- |
|
| 30 | -brother2270 is located in the SBGrid computing room. Printing will not work if |
|
| 31 | -your computer is connected to the HMS Wifi access point (HMS Private or |
|
| 32 | -Public). |
|
| 33 | - |
|
| 34 | - |
|
| 35 | - |
|
| 36 | -##Personal Desktop Computers: |
|
| 37 | -Personal (OS X / Windows?) systems (sch-jlchoi- |
|
| 38 | -imac, ps-wang-macmini, ps-sophia-imac, sb-liz-imac, ps-nozhat-macmini) are |
|
| 39 | -administered by the primary user, with support from SBGrid and HMS/BCMP IT. |
|
| 40 | - |
|
| 41 | - * SBGrid software will be installed in /programs. |
|
| 42 | - |
|
| 43 | - * All research data should be backed-up . This is an NIH and HMS regulation. |
|
| 44 | - |
|
| 45 | - * Visiting Students should use HMS [CrashPlan](http://it.hms.harvard.edu/pg.asp?pn=cpp_backup) for backing up their work directories. (use registration code JJRR-RHW7-UHJW-H7JM). |
|
| 46 | - |
|
| 47 | - * Postdocs and Graduate Students should always work from a DropBox folder. |
|
| 48 | - |
|
| 49 | -##Software: |
|
| 50 | - |
|
| 51 | - * personal computers and laptops running OS X can have [SBGrid software installed](http://forums.sbgrid.org/topic/updating-sbgrid-software-on-your-mac-from-sbgrid-central-server) |
|
| 52 | - * [HMS licensed software](https://rc.hms.harvard.edu/#downloads) (such as ChemOffice or MATLAB) |
|
| 53 | - * MS office is available on request from [](mailto:bcmpit@hms.harvard.edu)[bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu) |
|
| 54 | - * Geneious: Geneious is preinstalled with SBGrid software collection and Sliz lab has access to a shared database. Please email Piotr for the database login credentials. |
|
| 55 | - * Please use ReadCube for managing your references and we will purchase a Pro version for your use (Pro supports syncing files between multiple computers). |
|
| 56 | - |
|
| 57 | -#Linux Workstations |
|
| 58 | -Two linux workstations ([schl12][1] and psl2) are fully |
|
| 59 | -administered by SBGrid. ps2 (in the 3rd bay) can dual-boot to Windows 7. To |
|
| 60 | -login to linux systems, use your CMCD credentials. To login to the windows |
|
| 61 | -partition, use the credentials posted over the machine. |
|
| 62 | - |
|
| 63 | -[1]:for consistency, schl12 will be renamed to psl1 |
|
| 64 | - |
|
| 65 | -## Instrumentation Computers: |
|
| 66 | -Computers running our FPLCs (PS-FPLC1, PS-FPLC2, PS-FPLC3) are managed by HMS IT and backups are done on a daily basis using CrashPlan. They can print to the laboratory printer. |
|
| 67 | - |
|
| 68 | -Sliz lab also has access to crystallization-room computers (Gryphon |
|
| 69 | -controller, unknown system) Those computers are also managed by HMS IT and |
|
| 70 | -backed-up using CrashPlan. |
|
| 71 | - |
|
| 72 | - |
|
| 73 | -## Support: |
|
| 74 | - |
|
| 75 | -There are several options for support: |
|
| 76 | - |
|
| 77 | - 1. Please review SBGrid and CMCD support forums on the SBGrid website: forums.sbgrid.org |
|
| 78 | - 2. For assistance with Linux workstations and SBGrid network please contact SBGrid ( [help@sbgrid.org](mailto:help@sbgrid.org) ). In most cases Pete Meyer or Justin O’Connor will respond to your request. |
|
| 79 | - 3. For assistance with printing and your personal desktop please contact HMS IT at [bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu) . In most cases Peter Cobb will respond to your requests. |
|
| 80 | - 4. For assistance with the structural biology software please contact [bugs@sbgrid.org](mailto:bugs@sbgrid.org) (Rob and Jason). |
|
| 81 | - |
|
| 82 | - |
|
| 83 | -## Other Resources: |
|
| 84 | - |
|
| 85 | - * SBGrid.org website |
|
| 86 | - |
|
| 87 | - * rc.hms.harvard.edu - Harvard Medical School Research Computing Support |
|
| 88 | - |
|
| 89 | -## Communication: |
|
| 90 | - |
|
| 91 | - * All members of Sliz lab are signed up for the Sliz lab mailing lists and the BCMP mailing lists. |
|
| 92 | - * You will also receive a copy of SBGrid monthly newsletter. |
|
| 93 | - * e-mail: Goup members should use hkl.hms.harvard.edu account as the institutional/work email account. You should forward other accounts (e.g. hms.harvard.edu) to HKL. |
|
| 94 | - |
old/howto-springer-lab-bch.md
| ... | ... | @@ -1,59 +0,0 @@ |
| 1 | -# HOWTO, Springer/Wu/Hur Lab, BCH |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | -## Site Overview: |
|
| 4 | -Members of the Springer, Wu and Hur Labs at the Children’s Hospital Boston |
|
| 5 | -have access to six Linux workstations; all running SBGrid Software Collection |
|
| 6 | -(see below). The Linux computers share authentication and data directories and |
|
| 7 | -can be accessed remotely by SSH (see |
|
| 8 | -[instructions](http://forums.sbgrid.org/topic/remote-access-to-linux- |
|
| 9 | -computers)). |
|
| 10 | - |
|
| 11 | -Research Computing support is provided by SBGrid - contact them |
|
| 12 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 13 | - |
|
| 14 | -## Shared Workstations: |
|
| 15 | - |
|
| 16 | -Name|OS|Hardware Configuration|Location|Notes |
|
| 17 | ----|---|---|---|--- |
|
| 18 | -tsl1|Sci Linux 6.5|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer |
|
| 19 | -tsl2|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer |
|
| 20 | -tsl3|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer |
|
| 21 | -tsl4|Sci Linux 6.4|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer |
|
| 22 | -sun|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro FX 3700| CLS 03098|Last checked: 11/19/2014, Owned by Wu |
|
| 23 | -moon|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Wu |
|
| 24 | - |
|
| 25 | -## Data Backups: |
|
| 26 | - |
|
| 27 | -Full and incremental backups of SBGrid file servers are conducted. This |
|
| 28 | -includes your home and data directories. In general, backups are kept for |
|
| 29 | -three months, and then are stored on physical media for archival purposes. If |
|
| 30 | -you need a file restored, please contact SBGrid |
|
| 31 | -[here](https://sbgrid.org/help/?tab=contact-us). |
|
| 32 | - |
|
| 33 | -#Printing: |
|
| 34 | - |
|
| 35 | -A Xerox Phaser 6700DN is located in the hallway outside CLS 03098. If you are |
|
| 36 | -having issues with printing, please contact SBGrid |
|
| 37 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 38 | - |
|
| 39 | -#Remote access: |
|
| 40 | - |
|
| 41 | -Please follow [this link](http://forums.sbgrid.org/topic/remote-access-to- |
|
| 42 | -linux-computers) for details on how to remotely connect to the workstations. |
|
| 43 | - |
|
| 44 | -##Networking and General IT Support: |
|
| 45 | - |
|
| 46 | -Contact Children’s help desk at (617) 919 4357 or at |
|
| 47 | -[](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu) |
|
| 48 | -. |
|
| 49 | - |
|
| 50 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 51 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 52 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 53 | - |
|
| 54 | - |
|
| 55 | - |
|
| 56 | - |
|
| 57 | - |
|
| 58 | - |
|
| 59 | - |
old/howto-structural-biol-core-dhe-paganon-lab-dfci.md
| ... | ... | @@ -1,69 +0,0 @@ |
| 1 | -# HOWTO, Dhe-Paganon Lab, DFCI |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | - |
|
| 4 | -## Site Overview: |
|
| 5 | - |
|
| 6 | -Members of the Dhe-Paganon Lab at the Dana Farber Cancer Institute have access |
|
| 7 | -to a Linux workstation running a large collection of structural biology |
|
| 8 | -software. It shares authentication and data directories. |
|
| 9 | - |
|
| 10 | -Lab members can use SBGrid machines in the Eck lab as well. |
|
| 11 | - |
|
| 12 | -The lab is located at the Longwood Center building. |
|
| 13 | - |
|
| 14 | -Research Computing support is provided by SBGrid. Pl ease contact SBGrid |
|
| 15 | -[here](https://sbgrid.org/help/?tab=contact-us). |
|
| 16 | - |
|
| 17 | - |
|
| 18 | -## Workstations: |
|
| 19 | - |
|
| 20 | -Name|OS|Hardware Configuration|Location|Notes |
|
| 21 | ----|---|---|---|--- |
|
| 22 | -sdp1|Sci Linux 6.5|Intel Core i7 at 3.70GHz. 4 cores. 16 GB or RAM. Nvidia Quadro K4000. | Graphics room (Longwood Center)|Last checked: 03/01/2015 |
|
| 23 | - |
|
| 24 | -## Data Backups: |
|
| 25 | - |
|
| 26 | -Backups on the linux workstations are performed on a regular basis by the |
|
| 27 | -research computing group at DFCI. If you have any questions about backups, |
|
| 28 | -need files restored, or have any general issue regarding backups, contact the |
|
| 29 | -Research Computing group via this web page: [Help Me - DFCI Reseach |
|
| 30 | -Computing](http://research4.dfci.harvard.edu/content/helpme) . |
|
| 31 | - |
|
| 32 | -Backups on Macs are managed by SBGrid. Pl ease contact SBGrid |
|
| 33 | -[here](https://sbgrid.org/help/?tab=contact-us) for more information. |
|
| 34 | -Instructions on how to setup your Mac computer can be found |
|
| 35 | -[here](http://here) . |
|
| 36 | - |
|
| 37 | -##Printing: |
|
| 38 | - |
|
| 39 | -A Xerox Phaser 8860 is available for printing near the admin office. If you |
|
| 40 | -need your workstation configured for printing, Please contact SBGrid |
|
| 41 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 42 | - |
|
| 43 | -## X-Ray Data Collection: |
|
| 44 | - |
|
| 45 | -Plum and Aqua are workstations designated for data collection, and are located |
|
| 46 | -in the X-Ray room. These machines have custom local software installs to |
|
| 47 | -interact with the Marresearch scanner. |
|
| 48 | - |
|
| 49 | -HKL2000 can be accessed and run on Plum and Aqua, and mjel12. |
|
| 50 | - |
|
| 51 | -Please contact Mike Eck to obtain guest privileges. |
|
| 52 | - |
|
| 53 | -## Remote Access: |
|
| 54 | - |
|
| 55 | -External SSH access is available at red.dfci.harvard.edu. |
|
| 56 | - |
|
| 57 | -## Networking and General IT Support: |
|
| 58 | - |
|
| 59 | -To report problems regarding the network at DFCI, or general computing |
|
| 60 | -support, contact the Partners Healthcare Help desk at: |
|
| 61 | -[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only |
|
| 62 | -works from a Partners network connection) |
|
| 63 | - |
|
| 64 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 65 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 66 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 67 | - |
|
| 68 | - |
|
| 69 | - |
old/howto-wei-lab.md
| ... | ... | @@ -1,48 +0,0 @@ |
| 1 | -# HOWTO, Wei Lab, Genzyme Corp |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | - |
|
| 4 | -## Site Overview: |
|
| 5 | - |
|
| 6 | -Members of the Wei lab at Genzyme Corporation have access to two Linux |
|
| 7 | -computers running a large collection of structural biology software. Both |
|
| 8 | -computers share authentication and data directories and can be only accessed |
|
| 9 | -locally from within the lab. Research Computing support is provided by |
|
| 10 | -[SBGrid](https://sbgrid.org/) . Please contact SBGrid |
|
| 11 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 12 | - |
|
| 13 | -## Backups |
|
| 14 | - |
|
| 15 | -Data backup is performed by the Genzyme IT department. |
|
| 16 | - |
|
| 17 | -## Workstations: |
|
| 18 | - |
|
| 19 | -Name|OS|Hardware Configuration|Location|Notes |
|
| 20 | ----|---|---|---|--- |
|
| 21 | -montana|CentOS 6.6| | Wei's office |Last checked: 03/02/2015 |
|
| 22 | -colorado|Sci Linux 6.6| | Yanfeng's office|Last checked: 03/02/2015 |
|
| 23 | -gpenguin|Sci Linux 6.6| | Dana's desk|Last checked: 03/02/2015 |
|
| 24 | - |
|
| 25 | -##User Accounts: |
|
| 26 | -To create or delete your account, please refer to this |
|
| 27 | -[page](http://forums.sbgrid.org/topic/new-accounts) . To change your password |
|
| 28 | -please use the yppasswd command on one of the workstations. |
|
| 29 | - |
|
| 30 | -##Using SBGrid programs: |
|
| 31 | - |
|
| 32 | -All applications are located in /programs directory and are configured to run |
|
| 33 | -without additional settings. |
|
| 34 | - |
|
| 35 | -Most of the software titles installed in the SBGrid Suite have several |
|
| 36 | -versions available. Typically, we try to provide at least three versions of |
|
| 37 | -each software package, although very old or very new applications may have |
|
| 38 | -fewer versions. To override the default version, follow these instructions. |
|
| 39 | - |
|
| 40 | -Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid- |
|
| 41 | -programs) if you need additional information on how to run SBGrid programs |
|
| 42 | -locally or remotely on your machine. |
|
| 43 | - |
|
| 44 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 45 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 46 | - |
|
| 47 | - |
|
| 48 | - |
old/howto-wucherpfennig-lab-dfci.md
| ... | ... | @@ -1,65 +0,0 @@ |
| 1 | -# HOWTO, Wucherpfennig Lab, DFCI |
|
| 2 | -This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful. |
|
| 3 | - |
|
| 4 | -## Site Overview: |
|
| 5 | -Members of the Wucherpfennig Lab at the Dana Farber Cancer Institute have |
|
| 6 | -access to a Linux workstation in the wet lab, running a large collection of |
|
| 7 | -structural biology software. It shares authentication and data directories and |
|
| 8 | -can be only accessed locally from within the lab. |
|
| 9 | - |
|
| 10 | -Research Computing support is provided by SBGrid. Please contact SBGrid |
|
| 11 | -[here](https://sbgrid.org/help/?tab=contact-us) . |
|
| 12 | - |
|
| 13 | -## Using SBGrid programs: |
|
| 14 | - |
|
| 15 | -All applications are located in /programs directory and are configured to run |
|
| 16 | -without additional settings. In most cases, you will easily be able to run any |
|
| 17 | -program in the collection by opening up a terminal shell, and typing the name |
|
| 18 | -of the program that you want to run. Linux applications are installed in the |
|
| 19 | -/programs/i386-linux subdirectory. |
|
| 20 | - |
|
| 21 | -Most of the software titles installed in the SBGrid Suite have several |
|
| 22 | -versions available. Typically, we try to provide at least three versions of |
|
| 23 | -each software package, although very old or very new applications may have |
|
| 24 | -fewer versions. To override the default version, follow [these |
|
| 25 | -instructions](http://forums.sbgrid.org/topic/overriding-software-versions) . |
|
| 26 | - |
|
| 27 | -Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid- |
|
| 28 | -programs) if you need information on how to run SBGrid programs remotely or |
|
| 29 | -locally on your machine. |
|
| 30 | - |
|
| 31 | -## Data Backups: |
|
| 32 | - |
|
| 33 | -Backups on the linux workstations are performed on a regular basis by the |
|
| 34 | -research computing group at DFCI. If you have any questions about backups, |
|
| 35 | -need files restored, or have any general issue regarding backups, contact the |
|
| 36 | -Research Computing group via this web page: [Help Me - DFCI Reseach |
|
| 37 | -Computing](http://research4.dfci.harvard.edu/content/helpme) . |
|
| 38 | - |
|
| 39 | -## X-Ray Data Collection: |
|
| 40 | - |
|
| 41 | -Plum and Aqua are workstations designated for data collection, and are located |
|
| 42 | -in the X-Ray room. These machines have custom local software installs to |
|
| 43 | -interact with the Marresearch scanner. |
|
| 44 | - |
|
| 45 | -HKL2000 can be accessed and run on Plum, Aqua and mjel12. |
|
| 46 | - |
|
| 47 | -Please contact Mike Eck to obtain guest privileges. |
|
| 48 | - |
|
| 49 | - |
|
| 50 | - |
|
| 51 | -## Networking and General IT Support: |
|
| 52 | - |
|
| 53 | -To report problems regarding the network at DFCI, or general computing |
|
| 54 | -support, contact the Partners Healthcare Help desk at: |
|
| 55 | -[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only |
|
| 56 | -works from a Partners network connection) |
|
| 57 | - |
|
| 58 | -* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs) |
|
| 59 | -* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help) |
|
| 60 | -* [Other Resources](http://forums.sbgrid.org/topic/other-resources) |
|
| 61 | - |
|
| 62 | - |
|
| 63 | - |
|
| 64 | - |
|
| 65 | - |
old/images/sbgrid_small_logo.gif
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