QLogic OFED+ Host Software User Guide, Rev. B

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3–TrueScale Cluster Setup and Administration Host Environment Setup for MPI Configuring for ssh Running MPI programs with the command mpirun on an TrueScale cluster depends, by default, on secure shell ssh to launch node programs on the nodes. In QLogic MPI, mpirun uses the secure shell command ssh to start instances of the given MPI program on the remote compute nodes without the need for interactive password entry on every node. To use ssh, you must have generated Rivest, Shamir, Adleman (RSA) or Digital Signal Algorithm (DSA) keys, public and private. The public keys must be distributed and stored on all the compute nodes so that connections to the remote machines can be established without supplying a password. You or your administrator must set up the ssh keys and associated files on the cluster. There are two methods for setting up ssh on your cluster. The first method, the shosts.equiv mechanism, is typically set up by the cluster administrator. The second method, using ssh-agent, is more easily accomplished by an individual user. NOTE: • rsh can be used instead of ssh. To use rsh, set the environment variable MPI_SHELL=rsh. See “Environment Variables” on page 4-20 for information on setting environment variables. Also see “Shell Options” on page A-6 for information on setting shell options in mpirun. • rsh has a limit on the number of concurrent connections it can have, typically 255, which may limit its use on larger clusters. Configuring ssh and sshd Using shosts.equiv This section describes how the cluster administrator can set up ssh and sshd through the shosts.equiv mechanism. This method is recommended, provided that your cluster is behind a firewall and accessible only to trusted users. “Configuring for ssh Using ssh-agent” on page 3-32 shows how an individual user can accomplish the same thing using ssh-agent. The example in this section assumes the following: • Both the cluster nodes and the front end system are running the openssh package as distributed in current Linux systems. • All cluster end users have accounts with the same account name on the front end and on each node, by using Network Information Service (NIS) or another means of distributing the password file. • The front end used in this example is called ip-fe. 3-30 D000046-005 B
3–TrueScale Cluster Setup and Administration Host Environment Setup for MPI • Root or superuser access is required on ip-fe and on each node to configure ssh. • ssh, including the host’s key, has already been configured on the system ip-fe. See the sshd and ssh-keygen man pages for more information. To use shosts.equiv to configure ssg and sshd: 1. On the system ip-fe (the front end node), change the /etc/ssh/ssh_config file to allow host-based authentication. Specifically, this file must contain the following four lines, all set to yes. If the lines are already there but commented out (with an initial #), remove the #. RhostsAuthentication yes RhostsRSAAuthentication yes HostbasedAuthentication yes EnableSSHKeysign yes 2. On each of the TrueScale node systems, create or edit the file /etc/ssh/shosts.equiv, adding the name of the front end system. Add the line: ip-fe Change the file to mode 600 when you are finished editing. 3. On each of the TrueScale node systems, create or edit the file /etc/ssh/ssh_known_hosts. You will need to copy the contents of the file /etc/ssh/ssh_host_dsa_key.pub from ip-fe to this file (as a single line), and then edit that line to insert ip-fe ssh-dss at the beginning of the line. This is very similar to the standard known_hosts file for ssh. An example line might look like this (displayed as multiple lines, but a single line in the file): ip-fe ssh-dss AAzAB3NzaC1kc3MAAACBAPoyES6+Akk+z3RfCkEHCkmYuYzqL2+1nwo4LeTVW pCD1QsvrYRmpsfwpzYLXiSJdZSA8hfePWmMfrkvAAk4ueN8L3ZT4QfCTwqvHV vSctpibf8n aUmzloovBndOX9TIHyP/Ljfzzep4wL17+5hr1AHXldzrmgeEKp6ect1wxAAAA FQDR56dAKFA4WgAiRmUJailtLFp8swAAAIBB1yrhF5P0jO+vpSnZrvrHa0Ok+ Y9apeJp3sessee30NlqKbJqWj5DOoRejr2VfTxZROf8LKuOY8tD6I59I0vlcQ 812E5iw1GCZfNefBmWbegWVKFwGlNbqBnZK7kDRLSOKQtuhYbGPcrVlSjuVps fWEju64FTqKEetA8l8QEgAAAIBNtPDDwdmXRvDyc0gvAm6lPOIsRLmgmdgKXT GOZUZ0zwxSL7GP1nEyFk9wAxCrXv3xPKxQaezQKs+KL95FouJvJ4qrSxxHdd1 NYNR0DavEBVQgCaspgWvWQ8cL 0aUQmTbggLrtD9zETVU5PCgRlQL6I3Y5sCCHuO7/UvTH9nneCg== Change the file to mode 600 when you are finished editing. D000046-005 B 3-31
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QLogic OFED+ Host Software User Gui
Page 3 and 4: Table of Contents 1 Introduction Ho
Page 5 and 6: QLogic OFED+ Host Software User Gui
Page 15 and 16: Preface The QLogic OFED+ Host Softw
Page 17 and 18: Preface Technical Support Technical
Page 19 and 20: 1 Introduction How this Guide is Or
Page 21 and 22: 1-Introduction Interoperability QLo
Page 23 and 24: 2 Step-by-Step Cluster Setup and MP
Page 25 and 26: 3 TrueScale Cluster Setup and Admin
Page 27 and 28: 3-TrueScale Cluster Setup and Admin
Page 53: 3-TrueScale Cluster Setup and Admin
Page 63 and 64: 4 Running QLogic MPI on QLogic Adap
Page 65 and 66: 4-Running QLogic MPI on QLogic Adap
Page 91 and 92: 5 Using Other MPIs Introduction Thi
Page 93 and 94: 5-Using Other MPIs Open MPI Open MP
Page 95 and 96: 5-Using Other MPIs MVAPICH Further
Page 97 and 98: 5-Using Other MPIs Managing Open MP
Page 99 and 100: 5-Using Other MPIs Platform (Scali)
Page 101 and 102: 5-Using Other MPIs Intel MPI Intel
Page 103 and 104: 5-Using Other MPIs Intel MPI When u
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5-Using Other MPIs Improving Perfor
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6 Performance Scaled Messaging Intr
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6-Performance Scaled Messaging Usin
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7 Dispersive Routing Infiniband use
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7-Dispersive Routing • Static_Des
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8 gPXE gPXE Setup gPXE is an open s
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8-gPXE Preparing the DHCP Server in
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8-gPXE Netbooting Over InfiniBand P
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8-gPXE Netbooting Over InfiniBand W
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8-gPXE Netbooting Over InfiniBand #
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8-gPXE Netbooting Over InfiniBand #
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8-gPXE Netbooting Over InfiniBand T
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8-gPXE HTTP Boot Setup 5. Create an
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A mpirun Options Summary This secti
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A-mpirun Options Summary Quiescence
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A-mpirun Options Summary Tuning Opt
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A-mpirun Options Summary Format Opt
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B Benchmark Programs Several MPI pe
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B-Benchmark Programs Benchmark 2: M
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B-Benchmark Programs Benchmark 4: M
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C VirtualNIC Interface Configuratio
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C-VirtualNIC Interface Configuratio
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D SRP Configuration SRP Configurati
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D-SRP Configuration QLogic SRP Conf
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D-SRP Configuration OFED SRP Config
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E Integration with a Batch Queuing
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E-Integration with a Batch Queuing
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E-Integration with a Batch Queuing
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F Troubleshooting This appendix des
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F-Troubleshooting Kernel and Initia
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F-Troubleshooting Kernel and Initia
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F-Troubleshooting OpenFabrics and I
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F-Troubleshooting Performance Issue
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F-Troubleshooting QLogic MPI Troubl
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G ULP Troubleshooting Troubleshooti
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G-ULP Troubleshooting Troubleshooti
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H Write Combining Introduction Writ
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H-Write Combining MTRR Mapping and
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I Useful Programs and Files The mos
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I-Useful Programs and Files Summary
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I-Useful Programs and Files Common
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J Recommended Reading Reference mat
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Corporate Headquarters QLogic Corpo
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