forked from pmodels/mpich
-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.vin
836 lines (603 loc) · 31.4 KB
/
README.vin
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
MPICH Release %VERSION%
MPICH is a high-performance and widely portable implementation of the
MPI-3.1 standard from the Argonne National Laboratory. This release
has all MPI 3.1 functions and features required by the standard with
the exception of support for the "external32" portable I/O format and
user-defined data representations for I/O.
This README file should contain enough information to get you started
with MPICH. More extensive installation and user guides can be found
in the doc/installguide/install.pdf and doc/userguide/user.pdf files
respectively. Additional information regarding the contents of the
release can be found in the CHANGES file in the top-level directory,
and in the RELEASE_NOTES file, where certain restrictions are
detailed. Finally, the MPICH web site, http://www.mpich.org, contains
information on bug fixes and new releases.
1. Getting Started
2. Reporting Installation or Usage Problems
3. Compiler Flags
4. Alternate Channels and Devices
5. Alternate Process Managers
6. Alternate Configure Options
7. Testing the MPICH installation
8. Fault Tolerance
9. Developer Builds
10. Multiple Fortran compiler support
11. ABI Compatibility
12. Capability Sets
13. Threads
-------------------------------------------------------------------------
1. Getting Started
==================
The following instructions take you through a sequence of steps to get
the default configuration (ch3 device, nemesis channel (with TCP and
shared memory), Hydra process management) of MPICH up and running.
(a) You will need the following prerequisites.
- REQUIRED: This tar file mpich-%VERSION%.tar.gz
- REQUIRED: A C compiler (C99 support is required. See
https://wiki.mpich.org/mpich/index.php/Shifting_toward_C99)
- OPTIONAL: A C++ compiler, if C++ applications are to be used
(g++, etc.). If you do not require support for C++ applications,
you can disable this support using the configure option
--disable-cxx (configuring MPICH is described in step 1(d)
below).
- OPTIONAL: A Fortran compiler, if Fortran applications are to be
used (gfortran, ifort, etc.). If you do not require support for
Fortran applications, you can disable this support using
--disable-fortran (configuring MPICH is described in step 1(d)
below).
Also, you need to know what shell you are using since different shell
has different command syntax. Command "echo $SHELL" prints out the
current shell used by your terminal program.
(b) Unpack the tar file and go to the top level directory:
tar xzf mpich-%VERSION%.tar.gz
cd mpich-%VERSION%
If your tar doesn't accept the z option, use
gunzip mpich-%VERSION%.tar.gz
tar xf mpich-%VERSION%.tar
cd mpich-%VERSION%
(c) Choose an installation directory, say
/home/<USERNAME>/mpich-install, which is assumed to non-existent
or empty. It will be most convenient if this directory is shared
by all of the machines where you intend to run processes. If not,
you will have to duplicate it on the other machines after
installation.
(d) Configure MPICH specifying the installation directory:
for csh and tcsh:
./configure --prefix=/home/<USERNAME>/mpich-install |& tee c.txt
for bash and sh:
./configure --prefix=/home/<USERNAME>/mpich-install 2>&1 | tee c.txt
Bourne-like shells, sh and bash, accept "2>&1 |". Csh-like shell,
csh and tcsh, accept "|&". If a failure occurs, the configure
command will display the error. Most errors are straight-forward
to follow. For example, if the configure command fails with:
"No Fortran compiler found. If you don't need to build any
Fortran programs, you can disable Fortran support using
--disable-fortran. If you do want to build Fortran programs,
you need to install a Fortran compiler such as gfortran or
ifort before you can proceed."
... it means that you don't have a Fortran compiler :-). You will
need to either install one, or disable Fortran support in MPICH.
If you are unable to understand what went wrong, please go to step
(2) below, for reporting the issue to the MPICH developers and
other users.
(e) Build MPICH:
for csh and tcsh:
make |& tee m.txt
for bash and sh:
make 2>&1 | tee m.txt
This step should succeed if there were no problems with the
preceding step. Check file m.txt. If there were problems, do a
"make clean" and then run make again with V=1.
make V=1 |& tee m.txt (for csh and tcsh)
OR
make V=1 2>&1 | tee m.txt (for bash and sh)
Then go to step (2) below, for reporting the issue to the MPICH
developers and other users.
(f) Install the MPICH commands:
for csh and tcsh:
make install |& tee mi.txt
for bash and sh:
make install 2>&1 | tee mi.txt
This step collects all required executables and scripts in the bin
subdirectory of the directory specified by the prefix argument to
configure.
(g) Add the bin subdirectory of the installation directory to your
path in your startup script (.bashrc for bash, .cshrc for csh,
etc.):
for csh and tcsh:
setenv PATH /home/<USERNAME>/mpich-install/bin:$PATH
for bash and sh:
PATH=/home/<USERNAME>/mpich-install/bin:$PATH ; export PATH
Check that everything is in order at this point by doing:
which mpicc
which mpiexec
These commands should display the path to your bin subdirectory of
your install directory.
IMPORTANT NOTE: The install directory has to be visible at exactly
the same path on all machines you want to run your applications
on. This is typically achieved by installing MPICH on a shared
NFS file-system. If you do not have a shared NFS directory, you
will need to manually copy the install directory to all machines
at exactly the same location.
(h) MPICH uses a process manager for starting MPI applications. The
process manager provides the "mpiexec" executable, together with
other utility executables. MPICH comes packaged with multiple
process managers; the default is called Hydra.
Now we will run an MPI job, using the mpiexec command as specified
in the MPI standard. There are some examples in the install
directory, which you have already put in your path, as well as in
the directory mpich-%VERSION%/examples. One of them is the classic
CPI example, which computes the value of pi by numerical
integration in parallel.
To run the CPI example with 'n' processes on your local machine,
you can use:
mpiexec -n <number> ./examples/cpi
Test that you can run an 'n' process CPI job on multiple nodes:
mpiexec -f machinefile -n <number> ./examples/cpi
The 'machinefile' is of the form:
host1
host2:2
host3:4 # Random comments
host4:1
'host1', 'host2', 'host3' and 'host4' are the hostnames of the
machines you want to run the job on. The ':2', ':4', ':1' segments
depict the number of processes you want to run on each node. If
nothing is specified, ':1' is assumed.
More details on interacting with Hydra can be found at
http://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager
If you have completed all of the above steps, you have successfully
installed MPICH and run an MPI example.
-------------------------------------------------------------------------
2. Reporting Installation or Usage Problems
===========================================
[VERY IMPORTANT: PLEASE COMPRESS ALL FILES BEFORE SENDING THEM TO
US. DO NOT SPAM THE MAILING LIST WITH LARGE ATTACHMENTS.]
The distribution has been tested by us on a variety of machines in our
environments as well as our partner institutes. If you have problems
with the installation or usage of MPICH, please follow these steps:
1. First see the Frequently Asked Questions (FAQ) page at
http://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions to
see if the problem you are facing has a simple solution. Many common
problems and their solutions are listed here.
2. If you cannot find an answer on the FAQ page, look through previous
email threads on the [email protected] mailing list archive
(https://lists.mpich.org/mailman/listinfo/discuss). It is likely
someone else had a similar problem, which has already been resolved
before.
3. If neither of the above steps work, please send an email to
[email protected]. You need to subscribe to this list
(https://lists.mpich.org/mailman/listinfo/discuss) before sending an
email.
Your email should contain the following files. ONCE AGAIN, PLEASE
COMPRESS BEFORE SENDING, AS THE FILES CAN BE LARGE. Note that,
depending on which step the build failed, some of the files might not
exist.
mpich-%VERSION%/c.txt (generated in step 1(d) above)
mpich-%VERSION%/m.txt (generated in step 1(e) above)
mpich-%VERSION%/mi.txt (generated in step 1(f) above)
mpich-%VERSION%/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/openpa/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/mpl/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/pm/hydra/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/pm/hydra/tools/topo/hwloc/hwloc/config.log (generated in step 1(d) above)
DID WE MENTION? DO NOT FORGET TO COMPRESS THESE FILES!
If you have compiled MPICH and are having trouble running an
application, please provide the output of the following command in
your email.
mpiexec -info
Finally, please include the actual error you are seeing when running
the application, including the mpiexec command used, and the host
file. If possible, please try to reproduce the error with a smaller
application or benchmark and send that along in your bug report.
4. If you have found a bug in MPICH, you can report it on our Github
page (https://github.com/pmodels/mpich/issues).
-------------------------------------------------------------------------
3. Compiler Flags
=================
MPICH allows several sets of compiler flags to be used. The first
three sets are configure-time options for MPICH, while the fourth is
only relevant when compiling applications with mpicc and friends.
(a) CFLAGS, CPPFLAGS, CXXFLAGS, FFLAGS, FCFLAGS, LDFLAGS and LIBS
(abbreviated as xFLAGS): Setting these flags would result in the
MPICH library being compiled/linked with these flags and the flags
internally being used in mpicc and friends.
(b) MPICHLIB_CFLAGS, MPICHLIB_CPPFLAGS, MPICHLIB_CXXFLAGS,
MPICHLIB_FFLAGS, and MPICHLIB_FCFLAGS (abbreviated as
MPICHLIB_xFLAGS): Setting these flags would result in the MPICH
library being compiled with these flags. However, these flags will
*not* be used by mpicc and friends.
(c) MPICH_MPICC_CFLAGS, MPICH_MPICC_CPPFLAGS, MPICH_MPICC_LDFLAGS,
MPICH_MPICC_LIBS, and so on for MPICXX, MPIF77 and MPIFORT
(abbreviated as MPICH_MPIX_FLAGS): These flags do *not* affect the
compilation of the MPICH library itself, but will be internally used
by mpicc and friends.
+--------------------------------------------------------------------+
| | | |
| | MPICH library | mpicc and friends |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| xFLAGS | Yes | Yes |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| MPICHLIB_xFLAGS | Yes | No |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| MPICH_MPIX_FLAGS | No | Yes |
| | | |
+--------------------+----------------------+------------------------+
All these flags can be set as part of configure command or through
environment variables.
Default flags
--------------
By default, MPICH automatically adds certain compiler optimizations
to MPICHLIB_CFLAGS. The currently used optimization level is -O2.
** IMPORTANT NOTE: Remember that this only affects the compilation of
the MPICH library and is not used in the wrappers (mpicc and friends)
that are used to compile your applications or other libraries.
This optimization level can be changed with the --enable-fast option
passed to configure. For example, to build an MPICH environment with
-O3 for all language bindings, one can simply do:
./configure --enable-fast=O3
Or to disable all compiler optimizations, one can do:
./configure --disable-fast
For more details of --enable-fast, see the output of "configure
--help".
For performance testing, we recommend the following flags:
./configure --enable-fast=O3,ndebug --disable-error-checking --without-timing \
--without-mpit-pvars
Examples
--------
Example 1:
./configure --disable-fast MPICHLIB_CFLAGS=-O3 MPICHLIB_FFLAGS=-O3 \
MPICHLIB_CXXFLAGS=-O3 MPICHLIB_FCFLAGS=-O3
This will cause the MPICH libraries to be built with -O3, and -O3
will *not* be included in the mpicc and other MPI wrapper script.
Example 2:
./configure --disable-fast CFLAGS=-O3 FFLAGS=-O3 CXXFLAGS=-O3 FCFLAGS=-O3
This will cause the MPICH libraries to be built with -O3, and -O3
will be included in the mpicc and other MPI wrapper script.
-------------------------------------------------------------------------
4. Alternate Channels and Devices
=================================
The communication mechanisms in MPICH are called "devices". MPICH
supports ch3 (default) and ch4 (experimental), as well as many
third-party devices that are released and maintained by other
institutes.
*************************************
ch3 device
**********
The ch3 device contains different internal communication options
called "channels". We currently support nemesis (default) and sock
channels.
nemesis channel
---------------
Nemesis provides communication using different networks (tcp, mx) as
well as various shared-memory optimizations. To configure MPICH with
nemesis, you can use the following configure option:
--with-device=ch3:nemesis
Shared-memory optimizations are enabled by default to improve
performance for multi-processor/multi-core platforms. They can be
disabled (at the cost of performance) either by setting the
environment variable MPICH_NO_LOCAL to 1, or using the following
configure option:
--enable-nemesis-dbg-nolocal
The --with-shared-memory= configure option allows you to choose how
Nemesis allocates shared memory. The options are "auto", "sysv", and
"mmap". Using "sysv" will allocate shared memory using the System V
shmget(), shmat(), etc. functions. Using "mmap" will allocate shared
memory by creating a file (in /dev/shm if it exists, otherwise /tmp),
then mmap() the file. The default is "auto". Note that System V
shared memory has limits on the size of shared memory segments so
using this for Nemesis may limit the number of processes that can be
started on a single node.
ofi network module
```````````````````
The ofi netmod provides support for the OFI network programming interface.
To enable, configure with the following option:
--with-device=ch3:nemesis:ofi
If the OFI include files and libraries are not in the normal search paths,
you can specify them with the following options:
--with-ofi-include= and --with-ofi-lib=
... or the if lib/ and include/ are in the same directory, you can use
the following option:
--with-ofi=
If the OFI libraries are shared libraries, they need to be in the
shared library search path. This can be done by adding the path to
/etc/ld.so.conf, or by setting the LD_LIBRARY_PATH variable in your
environment. It's also possible to set the shared library search path
in the binary. If you're using gcc, you can do this by adding
LD_LIBRARY_PATH=/path/to/lib
(and)
LDFLAGS="-Wl,-rpath -Wl,/path/to/lib"
... as arguments to configure.
sock channel
------------
sock is the traditional TCP sockets based communication channel. It
uses TCP/IP sockets for all communication including intra-node
communication. So, though the performance of this channel is worse
than that of nemesis, it should work on almost every platform. This
channel can be configured using the following option:
--with-device=ch3:sock
ch4 device
**********
The ch4 device contains different network and shared memory modules
for communication. We currently support the ofi and ucx network
modules, and posix shared memory module.
ofi network module
```````````````````
The ofi netmod provides support for the OFI network programming interface.
To enable, configure with the following option:
--with-device=ch4:ofi[:provider]
If the OFI include files and libraries are not in the normal search paths,
you can specify them with the following options:
--with-libfabric-include= and --with-libfabric-lib=
... or the if lib/ and include/ are in the same directory, you can use
the following option:
--with-libfabric=
If specifying the provider, the MPICH library will be optimized specifically
for the requested provider by removing runtime branches to determine
provider capabilities. Note that using this feature with a version of the
libfabric library older than that recommended with this version of MPICH is
unsupported and may result in unexpected behavior. This is also true when
using the environment variable MPIR_CVAR_OFI_USE_PROVIDER, which will also
do some optimization for the requested provider.
The currently expected version of libfabric is: %LIBFABRIC_VERSION%.
ucx network module
``````````````````
The ucx netmod provides support for the Unified Communication X
library. It can be built with the following configure option:
--with-device=ch4:ucx
If the UCX include files and libraries are not in the normal search paths,
you can specify them with the following options:
--with-ucx-include= and --with-ucx-lib=
... or the if lib/ and include/ are in the same directory, you can use
the following option:
--with-ucx=
By default, the UCX library throws warnings when the system does not
enable certain features that might hurt performance. These are
important warnings that might cause performance degradation on your
system. But you might need root privileges to fix some of them. If
you would like to disable such warnings, you can set the UCX log level
to "error" instead of the default "warn" by using:
UCX_LOG_LEVEL=error
export UCX_LOG_LEVEL
-------------------------------------------------------------------------
5. Alternate Process Managers
=============================
hydra
-----
Hydra is the default process management framework that uses existing
daemons on nodes (e.g., ssh, pbs, slurm, sge) to start MPI
processes. More information on Hydra can be found at
http://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager
gforker
-------
gforker is a process manager that creates processes on a single
machine, by having mpiexec directly fork and exec them. gforker is
mostly meant as a research platform and for debugging purposes, as it
is only meant for single-node systems.
slurm
-----
Slurm is an external process manager not distributed with
MPICH. MPICH's default process manager, hydra, has native support
for Slurm and you can directly use it in Slurm environments (it will
automatically detect Slurm and use Slurm capabilities). However, if
you want to use the Slurm-provided "srun" process manager, you can use
the "--with-pmi=slurm --with-pm=no" option with configure. Note that
the "srun" process manager that comes with Slurm uses an older PMI
standard which does not have some of the performance enhancements that
hydra provides in Slurm environments.
-------------------------------------------------------------------------
6. Alternate Configure Options
==============================
MPICH has a number of other features. If you are exploring MPICH as
part of a development project, you might want to tweak the MPICH
build with the following configure options. A complete list of
configuration options can be found using:
./configure --help
-------------------------------------------------------------------------
7. Testing the MPICH installation
==================================
To test MPICH, we package the MPICH test suite in the MPICH
distribution. You can run the test suite using:
make testing
The results summary will be placed in test/summary.xml
-------------------------------------------------------------------------
8. Fault Tolerance
==================
MPICH has some tolerance to process failures, and supports
checkpointing and restart.
Tolerance to Process Failures
-----------------------------
The features described in this section should be considered
experimental. Which means that they have not been fully tested, and
the behavior may change in future releases. The below notes are some
guidelines on what can be expected in this feature:
- ERROR RETURNS: Communication failures in MPICH are not fatal
errors. This means that if the user sets the error handler to
MPI_ERRORS_RETURN, MPICH will return an appropriate error code in
the event of a communication failure. When a process detects a
failure when communicating with another process, it will consider
the other process as having failed and will no longer attempt to
communicate with that process. The user can, however, continue
making communication calls to other processes. Any outstanding
send or receive operations to a failed process, or wildcard
receives (i.e., with MPI_ANY_SOURCE) posted to communicators with a
failed process, will be immediately completed with an appropriate
error code.
- COLLECTIVES: For collective operations performed on communicators
with a failed process, the collective would return an error on
some, but not necessarily all processes. A collective call
returning MPI_SUCCESS on a given process means that the part of the
collective performed by that process has been successful.
- PROCESS MANAGER: If used with the hydra process manager, hydra will
detect failed processes and notify the MPICH library. Users can
query the list of failed processes using MPIX_Comm_group_failed().
This functions returns a group consisting of the failed processes
in the communicator. The function MPIX_Comm_remote_group_failed()
is provided for querying failed processes in the remote processes
of an intercommunicator.
Note that hydra by default will abort the entire application when
any process terminates before calling MPI_Finalize. In order to
allow an application to continue running despite failed processes,
you will need to pass the -disable-auto-cleanup option to mpiexec.
- FAILURE NOTIFICATION: THIS IS AN UNSUPPORTED FEATURE AND WILL
ALMOST CERTAINLY CHANGE IN THE FUTURE!
In the current release, hydra notifies the MPICH library of failed
processes by sending a SIGUSR1 signal. The application can catch
this signal to be notified of failed processes. If the application
replaces the library's signal handler with its own, the application
must be sure to call the library's handler from it's own
handler. Note that you cannot call any MPI function from inside a
signal handler.
Checkpoint and Restart
----------------------
MPICH supports checkpointing and restart fault-tolerance using BLCR.
CONFIGURATION
First, you need to have BLCR version 0.8.2 or later installed on your
machine. If it's installed in the default system location, you don't
need to do anything.
If BLCR is not installed in the default system location, you'll need
to tell MPICH's configure where to find it. You might also need to
set the LD_LIBRARY_PATH environment variable so that BLCR's shared
libraries can be found. In this case add the following options to
your configure command:
--with-blcr=<BLCR_INSTALL_DIR>
LD_LIBRARY_PATH=<BLCR_INSTALL_DIR>/lib
where <BLCR_INSTALL_DIR> is the directory where BLCR has been
installed (whatever was specified in --prefix when BLCR was
configured).
After it's configured compile as usual (e.g., make; make install).
Note, checkpointing is only supported with the Hydra process manager.
VERIFYING CHECKPOINTING SUPPORT
Make sure MPICH is correctly configured with BLCR. You can do this
using:
mpiexec -info
This should display 'BLCR' under 'Checkpointing libraries available'.
CHECKPOINTING THE APPLICATION
There are two ways to cause the application to checkpoint. You can ask
mpiexec to periodically checkpoint the application using the mpiexec
option -ckpoint-interval (seconds):
mpiexec -ckpointlib blcr -ckpoint-prefix /tmp/app.ckpoint \
-ckpoint-interval 3600 -f hosts -n 4 ./app
Alternatively, you can also manually force checkpointing by sending a
SIGUSR1 signal to mpiexec.
The checkpoint/restart parameters can also be controlled with the
environment variables HYDRA_CKPOINTLIB, HYDRA_CKPOINT_PREFIX and
HYDRA_CKPOINT_INTERVAL.
To restart a process:
mpiexec -ckpointlib blcr -ckpoint-prefix /tmp/app.ckpoint -f hosts -n 4 -ckpoint-num <N>
where <N> is the checkpoint number you want to restart from.
These instructions can also be found on the MPICH wiki:
http://wiki.mpich.org/mpich/index.php/Checkpointing
-------------------------------------------------------------------------
9. Developer Builds
===================
For MPICH developers who want to directly work on the primary version
control system, there are a few additional steps involved (people
using the release tarballs do not have to follow these steps). Details
about these steps can be found here:
http://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH
-------------------------------------------------------------------------
10. Multiple Fortran compiler support
=====================================
If the C compiler that is used to build MPICH libraries supports both
multiple weak symbols and multiple aliases of common symbols, the
Fortran binding can support multiple Fortran compilers. The
multiple weak symbols support allow MPICH to provide different name
mangling scheme (of subroutine names) required by differen Fortran
compilers. The multiple aliases of common symbols support enables
MPICH to equal different common block symbols of the MPI Fortran
constant, e.g. MPI_IN_PLACE, MPI_STATUS_IGNORE. So they are understood
by different Fortran compilers.
Since the support of multiple aliases of common symbols is
new/experimental, users can disable the feature by using configure
option --disable-multi-aliases if it causes any undesirable effect,
e.g. linker warnings of different sizes of common symbols, MPIFCMB*
(the warning should be harmless).
We have only tested this support on a limited set of
platforms/compilers. On linux, if the C compiler that builds MPICH is
either gcc or icc, the above support will be enabled by configure. At
the time of this writing, pgcc does not seem to have this multiple
aliases of common symbols, so configure will detect the deficiency and
disable the feature automatically. The tested Fortran compilers
include GNU Fortran compilers (gfortan), Intel Fortran compiler
(ifort), Portland Group Fortran compilers (pgfortran), Absoft Fortran
compilers (af90), and IBM XL fortran compiler (xlf). What this means
is that if mpich is built by gcc/gfortran, the resulting mpich library
can be used to link a Fortran program compiled/linked by another
fortran compiler, say pgf90, say through mpifort -fc=pgf90. As long
as the Fortran program is linked without any errors by one of these
compilers, the program shall be running fine.
-------------------------------------------------------------------------
11. ABI Compatibility
=====================
The MPICH ABI compatibility initiative was announced at SC 2014
(http://www.mpich.org/abi). As a part of this initiative, Argonne,
Intel, IBM and Cray have committed to maintaining ABI compatibility
with each other.
As a first step in this initiative, starting with version 3.1, MPICH
is binary (ABI) compatible with Intel MPI 5.0. This means you can
build your program with one MPI implementation and run with the other.
Specifically, binary-only applications that were built and distributed
with one of these MPI implementations can now be executed with the
other MPI implementation.
Some setup is required to achieve this. Suppose you have MPICH
installed in /path/to/mpich and Intel MPI installed in /path/to/impi.
You can run your application with mpich using:
% export LD_LIBRARY_PATH=/path/to/mpich/lib:$LD_LIBRARY_PATH
% mpiexec -np 100 ./foo
or using Intel MPI using:
% export LD_LIBRARY_PATH=/path/to/impi/lib:$LD_LIBRARY_PATH
% mpiexec -np 100 ./foo
This works irrespective of which MPI implementation your application
was compiled with, as long as you use one of the MPI implementations
in the ABI compatibility initiative.
-------------------------------------------------------------------------
12. Capability Sets
=====================
The CH4 device contains a feature called "capability sets" to simplify
configuration of MPICH on systems using the OFI netmod. This feature
configures MPICH to use a predetermined set of OFI features based on the
provider being used. Capability sets can be configured at compile time or
runtime. Compile time configuration provides better performance by
reducing unnecessary code branches, but at the cost of flexibility.
To configure at compile time, the device string should be amended to include
the OFI provider with the following option:
--with-device=ch4:ofi:sockets
This will setup the OFI netmod to use the optimal configuration for the
sockets provider, and will set various compile time constants. These settings
cannot be changed at runtime.
If runtime configuration is needed, continue to use the device string as before
(without the OFI provider extension) and set various environment variables to
achieve a similar configuration. To select the desired provider:
% export MPIR_CVAR_OFI_USE_PROVIDER=sockets
This will select the OFI provider and the associated MPICH capability set. To
change the preset configuration, there exists an extended set of environment
variables. As an example, the immediate data fields can be disabled by using
the environment variable:
% export MPIR_CVAR_OFI_ENABLE_TAGGED=0
For some configuration options (in particular, MPIR_CVAR_OFI_ENABLE_TAGGED and
MPIR_CVAR_OFI_ENABLE_RMA), a default build of MPICH using the CH4 OFI netmod
will fail if these options are not enabled. This is so that, for performance,
MPICH can assume that some commonly available features are enabled by the OFI
provider. If using a provider that does not support FI_TAGGED, FI_RMA, or
FI_DELIVERY_COMPLETE, a special configure flag must be provided to build in
support for workarounds for such features. Compile with --enable-legacy-ofi
to enable such workarounds.
A full list of capability set configuration variables can be found in the
environment variables README.envvar.
-------------------------------------------------------------------------
13. Threads
===========
MPICH supports multiple threading packages. The default is posix
threads (pthreads), but solaris threads, windows threads and argobots
are also supported.
To configure mpich to work with argobots threads, use the following
configure options:
--with-thread-package=argobots \
CFLAGS="-I<path_to_argobots/include>" \
LDFLAGS="-L<path_to_argobots/lib>"