今天使用Intel MPI运行程序时，报错： mpiexec_cooler: cannot connect to local mpd (/tmp/mpd2.console_cuiyb); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a console (-n option) 说是未启动 mpd 或是 mpd 启动不正确。 那么什么是 mpd 呢？ mpd=mutipurpose daemon，是 Intel MPI库中 用于启动并行任务的进程管理系统。在启动一个工作之前，首先需要在各个节点上启动 mpd 守护进程(mpd daemon)，使得各节点相连形成环。 也就是说在使用 Intel MPI 执行程序前，要先启动 mpd，命令如下： $mpdboot \ \ \ 如果在单节点上执行任务，直接运行 $mpdboot 即可。
在分子模拟中，当体系非常庞大时，单机计算就显得非常缓慢，这时候就要用到多核/多机并行运算。MPI就是一种很好的并行实现方式，它通过网络把许多计算机连接起来，把任务分配给许多CPU以实现加速。下面用一个例子说明在分子模拟中如何利用MPI来计算体系的能量。 假定体系有1 000 000个原子，那么要计算原子间总的相互作用就需要进行5$\times$10$^{11}$次计算，单机运行起来很慢。 do iAtom = 1, 1000000-1 do jAtom = iAtom + 1, 1000000 uTot = uTot + getEn(iAtom, jAtom) end do end do 但是如果我们有10个CPU，那么每个CPU只要计算$\frac{1}{10}$的相互作用就可以了，理论上可以提速十倍。对每台机器来说，只要运行 do iAtom = iProc + 1, 1000000-1, nProcs do jAtom = iAtom + 1, 1000000 uTot = uTot + getEn(iAtom, jAtom) end do end do 其中iProc是当前CPU的序号，nProcs是要使用的CPU的总数。每个CPU得到各自的结果后，用MPI_Reduce把大家的结果都加起来，就得到了体系的总能量。
Open MPI, MPICH2 Open MPI Information ompi_info --all #show all Open MPI info mpif90 -showme #show command line that would be invoked to compile the program mpif90 -showme:link #show linker flags that would be supplied to the Fortran 90 compiler mpif90 -showme:compile #show compiler flags that would be supplied to the Fortran 90 compiler Installation Instructions for Open MPI Mac OS X (via MacPorts) sudo port install openmpi Mac OS X (Compile from source) 1. Download openmpi-1.4.3.tar.gz from http://www.open-mpi.org/. 2. Extract the Open MPI source tar zxf openmpi-1.4.3.gz cd openmpi-1.4.3/ 3. Run the configure script using the following commands. Replace '1.4.3' with the version number of the openmpi .tar.gz/.tgz file which you downloaded from the internet. Replace /opt/openmpi with the folder of your choice. Optionally, you can specify which C/C++ compiler (such as gcc/g++ which comes with XCode) and its flags, as well as the Fortran 77/90 compiler. The '-m64' flag (gcc compilers only) specifies to build Open MPI for 64-bit architecture. ./configure --help #if you need to check the settings. mkdir build/ ../configure --prefix=/opt/openmpi CC=gcc CXX=g++ F77=gfortran FC=gfortran CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64 21 | tee config.out #../configure --prefix=/opt/openmpi 21 | tee config.out #if you wish to use the default settings. 4. Compile Open MPI from source using: make -j 21 | tee make.out #as a user with write permissions in the build tree. optional '-j' setting is for a parallel make. 5. Install Open MPI with: sudo make install 21 | tee install.out #as a user with write permissions to the install tree 6. Setup the enviroment with: export PATH="/opt/openmpi/bin:$PATH" export OPAL_PREFIX="/opt/openmpi " #optional 7. Check the installation with: which mpicc; which mpic++; which mpif90 #check that executables are in the correct path ompi_info to only just check the compilers, type: ompi_info | grep compiler 8. Run your code using any of the following three options: mpirun --prefix /opt/openmpi -np 4 ./a.out /opt/openmpi/bin/mpirun -np 4 ./a.out add "export PATH=/opt/openmpi/bin:$PATH" to $HOME/.bash_profile (if using bash) Additional configuration options from http://www.open-mpi.org/faq/?category=building: If you need to specify the compiler bindings, you'll need to change the ./configure option above as: ./configure --prefix=/opt/openmpi CC=icc CXX=icpc F77=ifort FC=ifort 21 | tee config.out #for Intel Compilers ./configure --prefix=/opt/openmpi CC=gcc CXX=g++ F77=gfortran FC=gfortran 21 | tee config.out #for GNU Compilers To produce 64 bit C,C++,F77, F90 objects ( for the GNU compiler suite) : ./configure --prefix=/opt/openmpi CC=gcc CXX=g++ F77=gfortran FC=gfortran CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64 21 | tee config.out Note that in future compiles, you'll need to specify '-m64', otherwise you'll get errors like: ld warning: in /opt/openmpi/lib/libmpi_f90.a, file is not of required architecture ld warning: in /opt/openmpi/lib/libmpi_f77.dylib, file is not of required architecture ld warning: in /opt/openmpi/lib/libmpi.dylib, file is not of required architecture ld warning: in /opt/openmpi/lib/libopen-rte.dylib, file is not of required architecture ld warning: in /opt/openmpi/lib/libopen-pal.dylib, file is not of required architecture To shift the entire openmpi tree to another folder, add the following to ~/.bash_profile : export OPAL_PREFIX=newfolder Troubleshooting : 1. Problem when mpic++ points to the binary of a different Open MPI installation (in /usr/local/bin) instead of the new Open MPI installation (/opt/openmpi/bin): $ mpic++ -m64 hellompi.cpp -o hellompi $ which mpic++ /usr/local/bin/mpic++ $ mpirun -np 1 ./hellompi mca: base: component_find: unable to open /opt/openmpi/lib/openmpi/mca_paffinity_darwin: file not found (ignored) mca: base: component_find: unable to open /opt/openmpi/lib/openmpi/mca_paffinity_test: file not found (ignored) mca: base: component_find: unable to open /opt/openmpi/lib/openmpi/mca_carto_auto_detect: file not found (ignored) mca: base: component_find: unable to open /opt/openmpi/lib/openmpi/mca_carto_file: file not found (ignored) -------------------------------------------------------------------------- It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): opal_carto_base_select failed -- Returned value -13 instead of OPAL_SUCCESS -------------------------------------------------------------------------- ,INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 77 ,INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 454 MPICH-2 Installing MPICH-2 with Intel Fortran/C++ (or another compiler) 1. Install Intel Compilers (ifort, icc, icpc), or another compiler 2. Download the appropriate MPICH2 source file. Extract the tar file and go to the folder: wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.4/mpich2-1.4.tar.gz tar -xzf mpich2-1.4.tar.gz cd mpich2-1.4/ 3. Use the environment variables to link MPICH2 to the appropriate Intel compilers: export FC=ifort export CC=icc export CXX=icc export RSH=ssh (change appropriately if another compiler is to be used). 4. Carry out the usual ./configure, make, make install (and optionally set up the path): ./configure --prefix=$HOME/usr make make install vi /etc/bashrc #as root (or vi ~/bashrc as non-root user) PATH=$HOME/usr/bin:$PATH From:https://sites.google.com/site/materialssimulation/home/coding-support/open-mpi
Efficient audit service outsourcing for data integrity in clouds Yan Zhua,b,∗, Hongxin Huc, Gail-Joon Ahnc, Stephen S. Yauc The Journal of Systems and Software 85 (2012) 1083– 1095 Abstract: Cloud-based outsourced storage relieves the client’s burden for storage management and maintenance by providing a comparably low-cost, scalable, location-independent platform. However, the fact that clients no longer have physical possession of data indicates that they are facing a potentially formidable risk for missing or corrupted data. To avoid the security risks, audit services are critical to ensure the integrity and availability of outsourced data and to achieve digital forensics and credibility on cloud computing. Provable data possession (PDP), which is a cryptographic technique for verifying the integrity of data without retrieving it at an untrusted server, can be used to realize audit services. In this paper, profiting from the interactive zero-knowledge proof system, we address the construction of an interactive PDP protocol to prevent the fraudulence of prover (soundness property) and the leakage of verified data (zero-knowledge property). We prove that our construction holds these properties based on the computation Diffie–Hellman assumption and the rewindable black-box knowledge extractor. We also propose an efficient mechanism with respect to probabilistic queries and periodic verification to reduce the audit costs per verification and implement abnormal detection timely. In addition, we present an efficient method for selecting an optimal parameter value to minimize computational overheads of cloud audit services. Our experimental results demonstrate the effectiveness of our approach. Keywords: Security, Cloud storage, Interactive proof system, Provable data possession, Audit service Efficient audit service outsourcing for data integrity in clouds.pdf
2009年马普同学会在中国农业大学成功举办 2009 年 7 月 19-21 日为期三天的马普同学会在金码大厦举行。此次马普同学会是由中国农业大学资源与环境学院陆雅海教授组织主办的学术交流会，旨在提供不同研究小组相互了解的机会，促进学术交流，寻求探索科学问题的合作机会。 与会者包括德国马普学会陆地微生物研究所所长、国际著名微生物学家 Ralf Conrad 教授，北京大学吴晓磊教授，中国农业大学陆雅海教授等其他曾在德国马普学会陆地微生物研究所（ MPI ）工作和学习过的老师和同学。活动首先由陆雅海教授致欢迎词，然后 Ralf Conrad 教授对于马普学会陆地微生物研究所现状及发展方向进行了详细的介绍，并做了题为 Isotope fractionation during the anaerobic consumption of acetate by methanogenic, sulfate- and sulfur-reducing microorganisms 的学术报告，其深厚的学术功底以及对于科学问题的把握给与会者留下了深刻印象。 学术部分按照大家于马普学习的时间顺序进行。首先各自用几张片子轻松自由地展示一下大家在马堡的生活学习回忆；然后介绍了目前岗位上的研究方向、研究进展、研究成果和今后展望等。来自于海南大学的但建国教授以一种轻松愉快的心情介绍了自己从事科学研究以后与甲烷之间的不解之缘；来自于北京大学工学院的吴晓磊教授的报告题目为 Dynamics of a saline soil bacterial community responding to heavy crude oil pollution and a combined biostimulation treatment ，分析了原油污染土壤上嗜盐微生物的动态变化以及生物刺激处理的后细菌群落变化；中国农业大学资源环境学院陆雅海教授结合本小组的研究工作对于水稻土中碳循环机理进行了阐述，报告中提出底物浓度的变化决定了不同温度下古菌和细菌的优势种群；华中师范大学的杨红副教授做了题为 Primary studies on symbiotic microorganisms in the intestinal tract of Reticulitermes chinensis Sndyer 的学术报告，报告中对于黑胸散白蚁内生肠道中共生微生物群落结构、固氮相关基因系统发育多样性进行了分析，而且从其肠道中分离到可培养的好氧以及兼性厌氧的微生物，最后并对今后的工作进行了展望；中科院青岛生物能源与过程研究所李福利研究员对于其研究小组的研究方向和研究进展进行了讲述，其报告着重提到可以利用麦糠进行能源燃料丁醇的发酵，因为其易于降解成为可溶性糖；其次还从不同的来源中分离得到多株可以分解利用木质素的酿酒酵母纯菌株；另外还分离得到可以产油的藻类多种；同样来自于中科院青岛生物能源与过程研究所的郭荣波研究员也是关注能源问题，如何从蓝藻中获得未来的新型可再生能源燃料氢气？目前的研究主要是筛选可以抗氧并具有活性的氢酶并对于获得的氢酶运用分子生物学方法进行修饰以期获得高活性的可以进行氢气大批量生产的氢酶。南京大学的季荣教授做了题为 Using 14 C -Tracer to Study Transformation of Organic Substances in Environment 的报告，利用 14C 标记技术研究外生物质在环境中的转化过程，包括腐殖质、儿茶酚和 nonylphenol 三种物质的转化。中科院南京土壤所的贾仲君教授其幽默风趣的讲话风格给大家留下了深刻的印象，在并在会上汇报了其在马普博士后工作期间的研究成果，题为 Bacteria rather than Archaea dominate ammonia oxidation in agricultural soils 的报告，步步深入的研究揭示了是细菌而非古菌在农田土壤氨氧化过程中起主要作用；并对于分子微生物生态学未来的发展方向发表了自己的观点与见解。来自于中国农大微生物分子生态学实验室的博士生裘琼芬做了题为 Identify Active Methanotrophs in the Rhizosphere and on the Roots of Rice 的报告，水稻根和水稻根际活跃存在的甲烷氧化菌，在水稻根际 I 型甲烷氧化菌占优势并活跃存在，而在水稻根部则是 II 型甲烷氧化菌占优势并活跃存在。最后中国农大微生物分子生态学实验室的博士生袁艳丽做了题为 Responses of methanogenic archaeal community to oxygen exposure in rice field soil 的报告，主要观点是水稻土在受到氧气胁迫后虽然甲烷的产生受到了明显的抑制，但是产甲烷古菌的群落结构却相对恒定，为阐明水稻土中受到氧气胁迫后碳循环提供了一定的理论基础解释。 学术报告结束后， Ralf Conrad 教授做了总结陈词，对于本次学术研讨会的成功举行给与了高度评价，并和大家一起回顾了他与中国的科学家们的学术交流历程。 最后几位与会者参观了中国农业大学分子微生物生态学实验室并进行了积极的交流。 撰稿人 袁艳丽
An Introduction to the Lab of Molecular Ecology MPI Partner Group, China Agricultural University (Yahai Lus Lab) The Lab of Molecular Ecology MPI Partner Group, China Agricultural University (CAU), was co-founded in Sep. 2006 by the Max Planck Institute for Terrestrial Microbiology of Marburg and the Key Laboratory of Plant and Soil Interactions of the Ministry of Education of China (MOE), which is affiliated to the College of Resources and Environmental Sciences at CAU. The faculty of the lab consists of one professor, chair professor, assistant professor and post doctor respectively, besides eight Ph.D. candidates and seven M.S. candidates. Prof. Yahai Lu, the director of the lab and the obtainer of the National Outstanding Youth Funds, was awarded both the title of New Century Excellent Talents and Changjiang Scholar by the MOE in 2006. Prof. Lu has worked at Philippines International Rice Research Institute, Japan Science and Technology Agency and MPI for years, where he conducted systematic researches on both biochemistry and microbiology of rice paddy soils. Since 2002, years of cooperative researches have been made between him and Prof. Ralf Conrad from MPI, who together not only developed and established the methodologies for microbial diversity on the interfaces between the rhizosphere and the soil, but also discovered and determined the key microbial groups and their mechanisms wherein, these results have been published in important academic magazines such as Science. In Sep.2006, the MPI Partner Group was co-founded by MPI and CAU based on the former cooperative foundation and achievements, to continue support and promote the leading edge cooperative researches between MPI and CAU. Prof. Lu was appointed the director of the partner group by Peter Gruss, the president of MPI. In the appointment letter, the president wrote that Dr. Lus scientific research has won very high international reputation, the MPI especially the Max Planck Institute for Terrestrial Microbiology of Marburg will support Dr. Lu to develop his partner group in the subsequent five years, he also expected the group to become an active scientific research centre in China and wished Dr. Lu successful researches at his new working place. In the same period, Prof. Ralf Conrad was appointed the chair professor of CAU by Zhangliang Chen, the president of CAU at that time. Prof. Conrad has been the director of the Max Planck Institute for Terrestrial Microbiology of Marburg since 1991, focused on soil microbiology and biogeochemistry. As a prestigious scientist in the world, he has published more than 250 scientific papers and 37 books, during which 35 Ph.D. students graduated from his lab, thus made outstanding academic accomplishments in his professional fields. He also won the lecture award of American Society for Microbiology in 1997 and the Francis E. Clark Distinguished Lecturer for the 2003 Soil Science Society of America Annual Meetings, soon after he became a board member for American Geophysical Union in 2005. He is the commissioner of ten international scientific committees such as the European Centre of Environmental Studies, and the former chief editor of FEMS Microbiology Ecology. Prof. Conrad has visited the partner group for once every year since 2006, where he gave us lectures and helped with our researches. The main topic of the lab is the microbial mechanisms of the environmental processes, which includes: 1. Molecular microbial ecology 2. Microbial diversity and their ecological functions in soil. 3. The microbial mechanisms of the carbon and nitrogen cycles. 4. Microbial remediation. Our tool box mainly consists of stable isotope probing and molecular biological techniques. The 211 and 985 projects of MOE have provided us EA-IRMS, Bechman Coulter Ultra-high-speed Centrifuge, ABI 3130 Sequencer, ABI 7900 Real Time PCR, etc. Multiple PCR instruments, DGGE equipment, Gel Imaging System and Ultra-low temperature refrigerator are available as well for conventional molecular analyses. (by Zhe Lv)
标签: MPI
