{"id":871,"date":"2013-01-22T10:57:25","date_gmt":"2013-01-22T08:57:25","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi"},"modified":"2015-08-14T11:50:08","modified_gmt":"2015-08-14T09:50:08","slug":"supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/","title":{"rendered":"SuperMicro GPU Servers and Mellanox Infiniband FDR \u2013 Connect X3-VPI"},"content":{"rendered":"

For the past couple of days we have been\r\nbusy with setting up and configuring x2 SuperMicro GPU servers 2U\r\nwhich consists of x4 Fermi Nvidia M2090 cards per server. Coupled with that\r\nwe installed a Mellanox Infiniband SX6036 externally managed switch\r\nwith Mellanox ConnectX-3 VPI HCA adapters in each server. The infiniband drivers used was from\r\nthe OpenFrabics<\/a> distribution OFED 1.5.4.1 which has support for Linux Kernel v3.<\/p>\r\n

I would like to document my findings\r\nabout setting up OFED on both Scientific Linux 5.8 and SLES 11.<\/p>\r\n

Installation of OFED under SL 5.8 (\r\nRHEL 5.8 ) <\/strong><\/p>\r\n

This was by far the most time consuming\r\nprocess for any troubleshooting exercise I have executed to date.\r\nBegin the installation by executing the .\/install script and select\r\nthe preferred option. The first thing to compile is the kernel-ib and\r\nkernel-devel. These will break. It should terminate with a error\r\ndisplayed below.<\/p>\r\n

pci.h:164: error: conflicting\r\ntypes for 'pci_pcie_cap OFED<\/strong><\/p>\r\n

OpenFrabics do not have a fix for it on\r\ntheir website from what we could see and decided to tinker around a\r\nbit. We found a developer hiding deep in the search archives of\r\ngoogle who had made modifications to the source RPM of the\r\nOFED-1.5.4.1 OFA kernel. The fix is as follows:<\/p>\r\n

1. tar xfvz OFED-1.5.4.1.tgz<\/p>\r\n

2. Change directory into the extracted\r\nOFED-1.5.4.1\/SRPMS<\/p>\r\n

3. Download the modified version from\r\nhere -\r\nhttp:\/\/troels.arvin.dk\/code\/ofa_kernel\/rhel5.8-enablement\/modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>\r\nand rename from modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>\r\nto ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>.\r\nDo not forget to backup the current file, although you can retrieve\r\nit from the tar.gz.<\/p>\r\n

4. Re-run the install script and you\r\nshould be good.<\/p>\r\n

You might also stumble across a compile\r\nerror of one of the networking modules from iWARP named \u201c cxgb3 and\r\ncxgb4 \u201c. I do not have these devices present so I can disable them\r\nfrom being compiled and causing the error. Disable the option in\r\nofed.conf . This file is created during the first run of the\r\ninstallation script. You can also find a sample copy of in the docs\/\r\nfolder. Edit the file, find the driver in the list and set the value\r\nto \u201cn\u201d. Re-run the installation script.<\/p>\r\n

The above issue with the \u201c cxgb3 and\r\ncxgb4 \u201c modules occurred on SLES 11 as well. Do not disable the\r\nkernel-ib and kernel-devel modules from being compiled as if you\r\ndisable these will not provide you with all the init scripts and\r\ncorrect kernel modules.<\/p>","protected":false},"excerpt":{"rendered":"

For the past couple of days we have been
\nbusy with setting up and configuring x2 SuperMicro GPU servers 2U
\nwhich consists of x4 Fermi Nvidia M2090 cards per server. Coupled with that
\nwe installed a Mellanox Infiniband SX6036 externally managed switch
\nwith Mellanox ConnectX-3 VPI HCA adapters in each server. The infiniband drivers used was from
\nthe OpenFrabics<\/a> distribution OFED 1.5.4.1 which has support for Linux Kernel v3. <\/p>\n

I would like to document my findings
\nabout setting up OFED on both Scientific Linux 5.8 and SLES 11. <\/p>\n

Installation of OFED under SL 5.8 (
\nRHEL 5.8 ) <\/strong>\n<\/p>\n

This was by far the most time consuming
\nprocess for any troubleshooting exercise I have executed to date.
\nBegin the installation by executing the .\/install script and select
\nthe preferred option. The first thing to compile is the kernel-ib and
\nkernel-devel. These will break. It should terminate with a error
\ndisplayed below.\n<\/p>\n

\t\t<\/strong><\/p>\n

\t\tpci.h:164: error: conflicting
\ntypes for ‘pci_pcie_cap OFED<\/strong><\/p>\n

OpenFrabics do not have a fix for it on
\ntheir website from what we could see and decided to tinker around a
\nbit. We found a developer hiding deep in the search archives of
\ngoogle who had made modifications to the source RPM of the
\nOFED-1.5.4.1 OFA kernel. The fix is as follows:\n<\/p>\n

<\/p>\n

1. tar xfvz OFED-1.5.4.1.tgz<\/p>\n

2. Change directory into the extracted
\nOFED-1.5.4.1\/SRPMS<\/p>\n

3. Download the modified version from
\nhere –
\nhttp:\/\/troels.arvin.dk\/code\/ofa_kernel\/rhel5.8-enablement\/modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>
\nand rename from modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>
\nto ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm<\/a>.
\nDo not forget to backup the current file, although you can retrieve
\nit from the tar.gz.\n<\/p>\n

4. Re-run the install script and you
\nshould be good.<\/p>\n

You might also stumble across a compile
\nerror of one of the networking modules from iWARP named “ cxgb3 and
\ncxgb4 “. I do not have these devices present so I can disable them
\nfrom being compiled and causing the error. Disable the option in
\nofed.conf . This file is created during the first run of the
\ninstallation script. You can also find a sample copy of in the docs\/
\nfolder. Edit the file, find the driver in the list and set the value
\nto “n”. Re-run the installation script.\n<\/p>\n

The above issue with the “ cxgb3 and
\ncxgb4 “ modules occurred on SLES 11 as well. Do not disable the
\nkernel-ib and kernel-devel modules from being compiled as if you
\ndisable these will not provide you with all the init scripts and
\ncorrect kernel modules.<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[4],"tags":[],"yoast_head":"\nSuperMicro GPU Servers and Mellanox Infiniband FDR \u2013 Connect X3-VPI - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"SuperMicro GPU Servers and Mellanox Infiniband FDR \u2013 Connect X3-VPI - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"For the past couple of days we have been busy with setting up and configuring x2 SuperMicro GPU servers 2U which consists of x4 Fermi Nvidia M2090 cards per server. Coupled with that we installed a Mellanox Infiniband SX6036 externally managed switch with Mellanox ConnectX-3 VPI HCA adapters in each server. The infiniband drivers used was from the OpenFrabics distribution OFED 1.5.4.1 which has support for Linux Kernel v3. I would like to document my findings about setting up OFED on both Scientific Linux 5.8 and SLES 11. Installation of OFED under SL 5.8 ( RHEL 5.8 ) This was by far the most time consuming process for any troubleshooting exercise I have executed to date. Begin the installation by executing the .\/install script and select the preferred option. The first thing to compile is the kernel-ib and kernel-devel. These will break. It should terminate with a error displayed below. pci.h:164: error: conflicting types for 'pci_pcie_cap OFED OpenFrabics do not have a fix for it on their website from what we could see and decided to tinker around a bit. We found a developer hiding deep in the search archives of google who had made modifications to the source RPM of the OFED-1.5.4.1 OFA kernel. The fix is as follows: 1. tar xfvz OFED-1.5.4.1.tgz 2. Change directory into the extracted OFED-1.5.4.1\/SRPMS 3. Download the modified version from here - http:\/\/troels.arvin.dk\/code\/ofa_kernel\/rhel5.8-enablement\/modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm and rename from modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm to ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm. Do not forget to backup the current file, although you can retrieve it from the tar.gz. 4. Re-run the install script and you should be good. You might also stumble across a compile error of one of the networking modules from iWARP named “ cxgb3 and cxgb4 “. I do not have these devices present so I can disable them from being compiled and causing the error. Disable the option in ofed.conf . This file is created during the first run of the installation script. You can also find a sample copy of in the docs\/ folder. Edit the file, find the driver in the list and set the value to “n”. Re-run the installation script. The above issue with the “ cxgb3 and cxgb4 “ modules occurred on SLES 11 as well. Do not disable the kernel-ib and kernel-devel modules from being compiled as if you disable these will not provide you with all the init scripts and correct kernel modules.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2013-01-22T08:57:25+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-08-14T09:50:08+00:00\" \/>\n<meta name=\"author\" content=\"Timothy Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Timothy Carr\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\"},\"author\":{\"name\":\"Timothy Carr\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/41f6cd039836d7741f2b82a7b7cfe8d0\"},\"headline\":\"SuperMicro GPU Servers and Mellanox Infiniband FDR \u2013 Connect X3-VPI\",\"datePublished\":\"2013-01-22T08:57:25+00:00\",\"dateModified\":\"2015-08-14T09:50:08+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\"},\"wordCount\":419,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/01\/22\/supermicro-gpu-servers-and-mellanox-infiniband-fdr-connect-x3-vpi\/\",\"name\":\"SuperMicro GPU Servers and Mellanox Infiniband FDR \u2013 Connect X3-VPI - 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Coupled with that we installed a Mellanox Infiniband SX6036 externally managed switch with Mellanox ConnectX-3 VPI HCA adapters in each server. The infiniband drivers used was from the OpenFrabics distribution OFED 1.5.4.1 which has support for Linux Kernel v3. I would like to document my findings about setting up OFED on both Scientific Linux 5.8 and SLES 11. Installation of OFED under SL 5.8 ( RHEL 5.8 ) This was by far the most time consuming process for any troubleshooting exercise I have executed to date. Begin the installation by executing the .\/install script and select the preferred option. The first thing to compile is the kernel-ib and kernel-devel. These will break. It should terminate with a error displayed below. pci.h:164: error: conflicting types for 'pci_pcie_cap OFED OpenFrabics do not have a fix for it on their website from what we could see and decided to tinker around a bit. We found a developer hiding deep in the search archives of google who had made modifications to the source RPM of the OFED-1.5.4.1 OFA kernel. The fix is as follows: 1. tar xfvz OFED-1.5.4.1.tgz 2. Change directory into the extracted OFED-1.5.4.1\/SRPMS 3. Download the modified version from here - http:\/\/troels.arvin.dk\/code\/ofa_kernel\/rhel5.8-enablement\/modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm and rename from modified-ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm to ofa_kernel-1.5.4.1-OFED.1.5.4.1.src.rpm. Do not forget to backup the current file, although you can retrieve it from the tar.gz. 4. Re-run the install script and you should be good. You might also stumble across a compile error of one of the networking modules from iWARP named “ cxgb3 and cxgb4 “. I do not have these devices present so I can disable them from being compiled and causing the error. Disable the option in ofed.conf . This file is created during the first run of the installation script. You can also find a sample copy of in the docs\/ folder. Edit the file, find the driver in the list and set the value to “n”. Re-run the installation script. The above issue with the “ cxgb3 and cxgb4 “ modules occurred on SLES 11 as well. 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