量子化学程序ORCA的安装方法

influenza

好的，谢谢啦！！Linux小白一个，呵呵！！

influenza

zjxitcc 发表于 2021-7-3 13:14
你的gview.exe前后单引号跨得太远了，中间openmpi环境变量颜色都异常了没看出来么

好的，谢谢啦！Linux小白一个，呵呵！！

influenza

zjxitcc 发表于 2021-7-3 13:14
你的gview.exe前后单引号跨得太远了，中间openmpi环境变量颜色都异常了没看出来么

可以了。不好意思。谢谢！！

qinsc

qinsc 发表于 2021-7-2 14:47
老师您好，我在运行ORCA5.0.0的时候报错

*** An error occurred in MPI_Type_match_size

问题已经解决，编译openmpi4.1.1的时候需要 gfortran 或者 ifort，仅有gcc就会出现这个问题。
编译openmpi之前需安装 gcc和gfortron。
原帖见 https://orcaforum.kofo.mpg.de/viewtopic.php?f=9&t=7566

wzkchem5

jitou11 发表于 2021-7-5 04:29
各位老师好!
这两天我尝试安装ORCA5.0但还是有问题，单核运行没发现啥问题，多核并行直接报错。测试的是本 ...

调用orca不能用mpirun，应该直接调用orca
orca主程序是串行的，它自己会用mpirun调用orca_gtoint_mpi、orca_scf_mpi等程序。你用mpirun调用orca就会导致嵌套并行，从而报错

annaqz

yurainingak 发表于 2018-12-21 11:07
在Linux下多个不同版本的openmpi是可以同时存在的，只需要在运行对应的ORCA版本时调用对应版本的openmpi ...

我不明白。我同时装了openmpi314和411，都在自定义目录下。在bash文件里把411的环境变量按照你写的这个修改了。但是which mpiexec的时候还是指向314.最开始如果两种mpi的环境变量设置完全一模一样，which mpiexec也还是指向314.这是为什么？要怎么修改呢？

乐平

Sob 老师好！
我按照此帖的步骤安装了 openmpi 4.1.1 版，

1. (base) [root@master orca_501]# ./configure --prefix=/public1/apps/openmpi_411 FC=ifort CC=icc CXX=icpc

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然后添加了环境变量。安装后检查版本正常，如下

1. (base) [wanghuan@n9 orca_jobs]$ mpiexec -V
   
2. mpiexec (OpenRTE) 4.1.1
   
3. 
   
4. Report bugs to http://www.open-mpi.org/community/help/
   
5. (base) [wanghuan@n9 orca_jobs]$
   
6. (base) [wanghuan@n9 orca_jobs]$

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然后按照帖子安装 orca 5.0.1，下载的是 orca_5_0_1_linux_x86-64_shared_openmpi411.tar.xz
似乎只用解压就够了，不用像其他程序 ./configure --prefix=/path/,   make， make install?

添加环境变量。

用帖子里的 CHHO 例子做测试，但是运行的时候出现如下错误，似乎与 openmpi 有关，报错代码如下：

1. (base) [wanghuan@n9 orca_jobs]$ orca test.inp > test.out
   
2. [n9:12018] mca_base_component_repository_open: unable to open mca_plm_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
   
3. [n9:12018] mca_base_component_repository_open: unable to open mca_ras_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
   
4. [n9:12026] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
   
5. [n9:12028] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
   
6. [n9:12027] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
   
7. [n9:12029] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
   
8. [n9:12028] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
   
9. [n9:12029] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
   
10. [n9:12027] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
11. [n9:12026] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
12. --------------------------------------------------------------------------
    
13. By default, for Open MPI 4.0 and later, infiniband ports on a device
    
14. are not used by default.  The intent is to use UCX for these devices.
    
15. You can override this policy by setting the btl_openib_allow_ib MCA parameter
    
16. to true.
    
17. 
    
18.   Local host:              n9
    
19.   Local adapter:           hfi1_0
    
20.   Local port:              1
    
21. 
    
22. --------------------------------------------------------------------------
    
23. --------------------------------------------------------------------------
    
24. WARNING: There was an error initializing an OpenFabrics device.
    
25. 
    
26.   Local host:   n9
    
27.   Local device: hfi1_0
    
28. --------------------------------------------------------------------------
    
29. [n9:12026] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
30. [n9:12029] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
31. [n9:12028] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
32. [n9:12027] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
33. [n9:12018] 3 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected
    
34. [n9:12018] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
    
35. [n9:12018] 3 more processes have sent help message help-mpi-btl-openib.txt / error in device init
    
36. [n9:12057] mca_base_component_repository_open: unable to open mca_plm_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
    
37. [n9:12057] mca_base_component_repository_open: unable to open mca_ras_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
    
38. [n9:12061] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
39. [n9:12061] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
40. [n9:12064] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
41. [n9:12063] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
42. [n9:12062] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
43. [n9:12064] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
44. [n9:12062] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
45. [n9:12063] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
46. --------------------------------------------------------------------------
    
47. By default, for Open MPI 4.0 and later, infiniband ports on a device
    
48. are not used by default.  The intent is to use UCX for these devices.
    
49. You can override this policy by setting the btl_openib_allow_ib MCA parameter
    
50. to true.
    
51. 
    
52.   Local host:              n9
    
53.   Local adapter:           hfi1_0
    
54.   Local port:              1
    
55. 
    
56. --------------------------------------------------------------------------
    
57. --------------------------------------------------------------------------
    
58. WARNING: There was an error initializing an OpenFabrics device.
    
59. 
    
60.   Local host:   n9
    
61.   Local device: hfi1_0
    
62. --------------------------------------------------------------------------
    
63. [n9:12061] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
64. [n9:12062] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
65. [n9:12063] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
66. [n9:12064] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
67. [n9:12057] 3 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected
    
68. [n9:12057] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
    
69. [n9:12057] 3 more processes have sent help message help-mpi-btl-openib.txt / error in device init
    
70. [n9:12079] mca_base_component_repository_open: unable to open mca_plm_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
    
71. [n9:12079] mca_base_component_repository_open: unable to open mca_ras_tm: libtorque.so.2: cannot open shared object file: No such file or directory (ignored)
    
72. [n9:12085] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
73. [n9:12084] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
74. [n9:12086] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
75. [n9:12083] mca_base_component_repository_open: unable to open mca_btl_usnic: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_usnic.so) (ignored)
    
76. [n9:12085] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
77. [n9:12086] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
78. [n9:12084] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
79. [n9:12083] mca_base_component_repository_open: unable to open mca_btl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_btl_ofi.so) (ignored)
    
80. --------------------------------------------------------------------------
    
81. By default, for Open MPI 4.0 and later, infiniband ports on a device
    
82. are not used by default.  The intent is to use UCX for these devices.
    
83. You can override this policy by setting the btl_openib_allow_ib MCA parameter
    
84. to true.
    
85. 
    
86.   Local host:              n9
    
87.   Local adapter:           hfi1_0
    
88.   Local port:              1
    
89. 
    
90. --------------------------------------------------------------------------
    
91. --------------------------------------------------------------------------
    
92. WARNING: There was an error initializing an OpenFabrics device.
    
93. 
    
94.   Local host:   n9
    
95.   Local device: hfi1_0
    
96. --------------------------------------------------------------------------
    
97. [n9:12083] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
98. [n9:12086] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
99. [n9:12085] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
    
100. [n9:12084] mca_base_component_repository_open: unable to open mca_mtl_ofi: /lib64/libfabric.so.1: version `FABRIC_1.3' not found (required by /public1/apps/openmpi_411/lib/openmpi/mca_mtl_ofi.so) (ignored)
     
101. [n9:12079] 3 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected
     
102. [n9:12079] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
     
103. [n9:12079] 3 more processes have sent help message help-mpi-btl-openib.txt / error in device init
     
104. (base) [wanghuan@n9 orca_jobs]$

复制代码

请问应该如何解决?

不过似乎能获得计算结果，出现以下文件：

1. (base) [wanghuan@n9 orca_jobs]$ la
   
2. total 736K
   
3. -rw-rw-r-- 1 wanghuan wanghuan  287 Jul 28  2021 test.inp
   
4. -rw-rw-r-- 1 wanghuan wanghuan  13K Jul 28  2021 test.densities
   
5. -rw-rw-r-- 1 wanghuan wanghuan 685K Jul 28  2021 test.gbw
   
6. -rw-rw-r-- 1 wanghuan wanghuan 3.3K Jul 28  2021 test_property.txt
   
7. -rw-rw-r-- 1 wanghuan wanghuan  24K Jul 28  2021 test.out

复制代码

从 test.out 文件来看，应该是正常结束了

1. (base) [wanghuan@n9 orca_jobs]$ tail -20 test.out
   
2. --------------------
   
3. Rotational spectrum
   
4. --------------------
   
5. 
   
6. Rotational constants in cm-1:     9.784569     1.218137     1.083274
   
7. Rotational constants in MHz : 293334.004965 36518.813588 32475.726275
   
8. 
   
9. Dipole components along the rotational axes:
   
10. x,y,z [a.u.] :    -0.864020    -0.000000     0.000000
    
11. x,y,z [Debye]:    -2.196164    -0.000000     0.000000
    
12. 
    
13. 
    
14. 
    
15. Timings for individual modules:
    
16. 
    
17. Sum of individual times         ...        2.965 sec (=   0.049 min)
    
18. GTO integral calculation        ...        1.117 sec (=   0.019 min)  37.7 %
    
19. SCF iterations                  ...        1.848 sec (=   0.031 min)  62.3 %
    
20.                              ****ORCA TERMINATED NORMALLY****
    
21. TOTAL RUN TIME: 0 days 0 hours 0 minutes 3 seconds 737 msec
    
22. (base) [wanghuan@n9 orca_jobs]$

复制代码

这是正常结束吗?

请指点，谢谢！

wzkchem5

乐平 发表于 2021-7-28 15:46
Sob 老师好！
我按照此帖的步骤安装了 openmpi 4.1.1 版，

是正常结束，结果是可以用的

乐平

wzkchem5 发表于 2021-7-28 18:32
是正常结束，结果是可以用的

谢谢！

openmpi 总是显示那么多 warning，看着很碍眼。
请问有没有方法解决呢？

任豹

小模型openmpi 并行计算成功,社长的模型也可以计算成功.大模型并行计算失败.归根结底还是机子上没有gfortran编译器.先安装gfortran编译器在安装orca,所有问题都解决了.我的版本是openmpi4.1.1,orca5.0.1.可能openmpi4需要gfortran编译器,之前的版本使用gcc就行.感谢楼上qinsc的回帖,不然不知道怎么解决!!!

wzkchem5

任豹 发表于 2021-11-13 17:45
小模型openmpi 并行计算成功,社长的模型也可以计算成功.大模型并行计算失败.归根结底还是机子上没有gfortra ...

准确来说是新版openmpi需要，orca本身一直是不需要gfortran的

任豹

wzkchem5 发表于 2021-11-14 16:45
准确来说是新版openmpi需要，orca本身一直是不需要gfortran的

对的,我搞错了.openmpi编译需要gfortran!

luzujia

重复sob老师给的算例没问题，换到另一个大点的模型就报MPI相关的错误，安装gfortran还是不行，请教老师们是什么原因。

wzkchem5

luzujia 发表于 2021-12-5 16:28
重复sob老师给的算例没问题，换到另一个大点的模型就报MPI相关的错误，安装gfortran还是不行，请教老师们是 ...

确定安装的是最新版openmpi吗？
如果确定，上传完整输出文件

luzujia

wzkchem5 发表于 2021-12-6 00:40
确定安装的是最新版openmpi吗？
如果确定，上传完整输出文件

安装的是openmpi411。所有输出文件已上传 testfile.rar (8.69 MB, 下载次数 Times of downloads: 17)

2021-12-6 08:58 上传 Uploaded

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