Skip to content

Commit abcecda

Browse files
mschubertmschubert
committed
package structure
1 parent a3d12e9 commit abcecda

12 files changed

+319
-49
lines changed

‎.Rbuildignore

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
\.gitignore
2+
CHANGES\.md
3+
Makefile
4+
README\.md
5+
^\.travis\.yml$

‎DESCRIPTION

+20
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
1+
Package: clustermq
2+
Title: ZeroMQ-powered cluster jobs
3+
Version: 0.0.1
4+
Author: Michael Schubert <[email protected]>
5+
Maintainer: Michael Schubert <[email protected]>
6+
Description: Transparent evaluation of function calls on workers that are
7+
submitted as LSF jobs without using network-mounted storage
8+
Depends:
9+
R (>= 3.0.2)
10+
Imports:
11+
tools,
12+
roxygen2
13+
License: Apache License (== 2.0) | file LICENSE
14+
LazyData: true
15+
Encoding: UTF-8
16+
Suggests:
17+
knitr,
18+
testthat
19+
VignetteBuilder: knitr
20+
RoxygenNote: 5.0.1

‎LICENSE

+202
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,202 @@
1+
2+
Apache License
3+
Version 2.0, January 2004
4+
http://www.apache.org/licenses/
5+
6+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
7+
8+
1. Definitions.
9+
10+
"License" shall mean the terms and conditions for use, reproduction,
11+
and distribution as defined by Sections 1 through 9 of this document.
12+
13+
"Licensor" shall mean the copyright owner or entity authorized by
14+
the copyright owner that is granting the License.
15+
16+
"Legal Entity" shall mean the union of the acting entity and all
17+
other entities that control, are controlled by, or are under common
18+
control with that entity. For the purposes of this definition,
19+
"control" means (i) the power, direct or indirect, to cause the
20+
direction or management of such entity, whether by contract or
21+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
22+
outstanding shares, or (iii) beneficial ownership of such entity.
23+
24+
"You" (or "Your") shall mean an individual or Legal Entity
25+
exercising permissions granted by this License.
26+
27+
"Source" form shall mean the preferred form for making modifications,
28+
including but not limited to software source code, documentation
29+
source, and configuration files.
30+
31+
"Object" form shall mean any form resulting from mechanical
32+
transformation or translation of a Source form, including but
33+
not limited to compiled object code, generated documentation,
34+
and conversions to other media types.
35+
36+
"Work" shall mean the work of authorship, whether in Source or
37+
Object form, made available under the License, as indicated by a
38+
copyright notice that is included in or attached to the work
39+
(an example is provided in the Appendix below).
40+
41+
"Derivative Works" shall mean any work, whether in Source or Object
42+
form, that is based on (or derived from) the Work and for which the
43+
editorial revisions, annotations, elaborations, or other modifications
44+
represent, as a whole, an original work of authorship. For the purposes
45+
of this License, Derivative Works shall not include works that remain
46+
separable from, or merely link (or bind by name) to the interfaces of,
47+
the Work and Derivative Works thereof.
48+
49+
"Contribution" shall mean any work of authorship, including
50+
the original version of the Work and any modifications or additions
51+
to that Work or Derivative Works thereof, that is intentionally
52+
submitted to Licensor for inclusion in the Work by the copyright owner
53+
or by an individual or Legal Entity authorized to submit on behalf of
54+
the copyright owner. For the purposes of this definition, "submitted"
55+
means any form of electronic, verbal, or written communication sent
56+
to the Licensor or its representatives, including but not limited to
57+
communication on electronic mailing lists, source code control systems,
58+
and issue tracking systems that are managed by, or on behalf of, the
59+
Licensor for the purpose of discussing and improving the Work, but
60+
excluding communication that is conspicuously marked or otherwise
61+
designated in writing by the copyright owner as "Not a Contribution."
62+
63+
"Contributor" shall mean Licensor and any individual or Legal Entity
64+
on behalf of whom a Contribution has been received by Licensor and
65+
subsequently incorporated within the Work.
66+
67+
2. Grant of Copyright License. Subject to the terms and conditions of
68+
this License, each Contributor hereby grants to You a perpetual,
69+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
70+
copyright license to reproduce, prepare Derivative Works of,
71+
publicly display, publicly perform, sublicense, and distribute the
72+
Work and such Derivative Works in Source or Object form.
73+
74+
3. Grant of Patent License. Subject to the terms and conditions of
75+
this License, each Contributor hereby grants to You a perpetual,
76+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
77+
(except as stated in this section) patent license to make, have made,
78+
use, offer to sell, sell, import, and otherwise transfer the Work,
79+
where such license applies only to those patent claims licensable
80+
by such Contributor that are necessarily infringed by their
81+
Contribution(s) alone or by combination of their Contribution(s)
82+
with the Work to which such Contribution(s) was submitted. If You
83+
institute patent litigation against any entity (including a
84+
cross-claim or counterclaim in a lawsuit) alleging that the Work
85+
or a Contribution incorporated within the Work constitutes direct
86+
or contributory patent infringement, then any patent licenses
87+
granted to You under this License for that Work shall terminate
88+
as of the date such litigation is filed.
89+
90+
4. Redistribution. You may reproduce and distribute copies of the
91+
Work or Derivative Works thereof in any medium, with or without
92+
modifications, and in Source or Object form, provided that You
93+
meet the following conditions:
94+
95+
(a) You must give any other recipients of the Work or
96+
Derivative Works a copy of this License; and
97+
98+
(b) You must cause any modified files to carry prominent notices
99+
stating that You changed the files; and
100+
101+
(c) You must retain, in the Source form of any Derivative Works
102+
that You distribute, all copyright, patent, trademark, and
103+
attribution notices from the Source form of the Work,
104+
excluding those notices that do not pertain to any part of
105+
the Derivative Works; and
106+
107+
(d) If the Work includes a "NOTICE" text file as part of its
108+
distribution, then any Derivative Works that You distribute must
109+
include a readable copy of the attribution notices contained
110+
within such NOTICE file, excluding those notices that do not
111+
pertain to any part of the Derivative Works, in at least one
112+
of the following places: within a NOTICE text file distributed
113+
as part of the Derivative Works; within the Source form or
114+
documentation, if provided along with the Derivative Works; or,
115+
within a display generated by the Derivative Works, if and
116+
wherever such third-party notices normally appear. The contents
117+
of the NOTICE file are for informational purposes only and
118+
do not modify the License. You may add Your own attribution
119+
notices within Derivative Works that You distribute, alongside
120+
or as an addendum to the NOTICE text from the Work, provided
121+
that such additional attribution notices cannot be construed
122+
as modifying the License.
123+
124+
You may add Your own copyright statement to Your modifications and
125+
may provide additional or different license terms and conditions
126+
for use, reproduction, or distribution of Your modifications, or
127+
for any such Derivative Works as a whole, provided Your use,
128+
reproduction, and distribution of the Work otherwise complies with
129+
the conditions stated in this License.
130+
131+
5. Submission of Contributions. Unless You explicitly state otherwise,
132+
any Contribution intentionally submitted for inclusion in the Work
133+
by You to the Licensor shall be under the terms and conditions of
134+
this License, without any additional terms or conditions.
135+
Notwithstanding the above, nothing herein shall supersede or modify
136+
the terms of any separate license agreement you may have executed
137+
with Licensor regarding such Contributions.
138+
139+
6. Trademarks. This License does not grant permission to use the trade
140+
names, trademarks, service marks, or product names of the Licensor,
141+
except as required for reasonable and customary use in describing the
142+
origin of the Work and reproducing the content of the NOTICE file.
143+
144+
7. Disclaimer of Warranty. Unless required by applicable law or
145+
agreed to in writing, Licensor provides the Work (and each
146+
Contributor provides its Contributions) on an "AS IS" BASIS,
147+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
148+
implied, including, without limitation, any warranties or conditions
149+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
150+
PARTICULAR PURPOSE. You are solely responsible for determining the
151+
appropriateness of using or redistributing the Work and assume any
152+
risks associated with Your exercise of permissions under this License.
153+
154+
8. Limitation of Liability. In no event and under no legal theory,
155+
whether in tort (including negligence), contract, or otherwise,
156+
unless required by applicable law (such as deliberate and grossly
157+
negligent acts) or agreed to in writing, shall any Contributor be
158+
liable to You for damages, including any direct, indirect, special,
159+
incidental, or consequential damages of any character arising as a
160+
result of this License or out of the use or inability to use the
161+
Work (including but not limited to damages for loss of goodwill,
162+
work stoppage, computer failure or malfunction, or any and all
163+
other commercial damages or losses), even if such Contributor
164+
has been advised of the possibility of such damages.
165+
166+
9. Accepting Warranty or Additional Liability. While redistributing
167+
the Work or Derivative Works thereof, You may choose to offer,
168+
and charge a fee for, acceptance of support, warranty, indemnity,
169+
or other liability obligations and/or rights consistent with this
170+
License. However, in accepting such obligations, You may act only
171+
on Your own behalf and on Your sole responsibility, not on behalf
172+
of any other Contributor, and only if You agree to indemnify,
173+
defend, and hold each Contributor harmless for any liability
174+
incurred by, or claims asserted against, such Contributor by reason
175+
of your accepting any such warranty or additional liability.
176+
177+
END OF TERMS AND CONDITIONS
178+
179+
APPENDIX: How to apply the Apache License to your work.
180+
181+
To apply the Apache License to your work, attach the following
182+
boilerplate notice, with the fields enclosed by brackets "[]"
183+
replaced with your own identifying information. (Don't include
184+
the brackets!) The text should be enclosed in the appropriate
185+
comment syntax for the file format. We also recommend that a
186+
file or class name and description of purpose be included on the
187+
same "printed page" as the copyright notice for easier
188+
identification within third-party archives.
189+
190+
Copyright [yyyy] [name of copyright owner]
191+
192+
Licensed under the Apache License, Version 2.0 (the "License");
193+
you may not use this file except in compliance with the License.
194+
You may obtain a copy of the License at
195+
196+
http://www.apache.org/licenses/LICENSE-2.0
197+
198+
Unless required by applicable law or agreed to in writing, software
199+
distributed under the License is distributed on an "AS IS" BASIS,
200+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
201+
See the License for the specific language governing permissions and
202+
limitations under the License.

‎Makefile

+28
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
1+
.PHONY: all
2+
all: documentation #vignettes
3+
4+
.PHONY: vignettes
5+
# Additionally build the *.md file, and copy all files
6+
vignettes: knit_all
7+
Rscript --no-save --no-restore -e "library(knitr); library(devtools); build_vignettes()"
8+
9+
rmd_files=$(wildcard vignettes/*.rmd)
10+
knit_results=$(patsubst vignettes/%.rmd,inst/doc/%.md,${rmd_files})
11+
12+
.PHONY: knit_all
13+
knit_all: inst/doc ${knit_results}
14+
cp -r vignettes/* inst/doc/
15+
16+
inst/doc:
17+
mkdir -p $@
18+
19+
inst/doc/%.md: vignettes/%.rmd
20+
Rscript --no-save --no-restore -e "library(knitr); knit('$<', '$@')"
21+
22+
.PHONY: documentation
23+
documentation:
24+
Rscript --no-save --no-restore -e "library(devtools); document()"
25+
26+
cleanall:
27+
${RM} -r inst/doc
28+
${RM} -r man

‎array_split.r ‎R/array_split.r

File renamed without changes.

‎array_subset.r ‎R/array_subset.r

File renamed without changes.

‎R/clustermq-package.r

+7
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
#' ZeroMQ-powered cluster jobs
2+
#'
3+
#' description goes here...
4+
#'
5+
#' @name clustermq
6+
#' @docType package
7+
NULL

‎master.r ‎R/master.r

+1
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@
3636
#' defaults to 1/sqrt(number_of_functon_calls)
3737
#' @param template Template file to use; will be "template_<template>.r" in this dir
3838
#' @return A list of whatever `fun` returned
39+
#' @export
3940
Q = function(fun, ..., const=list(), expand_grid=FALSE, seed=128965,
4041
memory=4096, n_jobs=NULL, job_size=NULL, split_array_by=NA, fail_on_error=TRUE,
4142
log_worker=FALSE, wait_time=NA, chunk_size=NA, template="LSF") {

‎process_args.r ‎R/process_args.r

File renamed without changes.

‎template_LSF.r ‎R/template_LSF.r

File renamed without changes.

‎R/worker.r

+56
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,56 @@
1+
#' R worker submitted as cluster job
2+
#'
3+
#' Do not call this manually, the master will do that
4+
#'
5+
#' @param worker_id The ID of the worker (usually just numbered)
6+
#' @param master The master address (tcp://ip:port)
7+
#' @param memlimit Maximum memory before throwing an error
8+
run_worker = function(worker_id, master, memlimit) {
9+
# worker_id = commandArgs(TRUE)[1]
10+
# master = commandArgs(TRUE)[2]
11+
# memlimit = as.integer(commandArgs(TRUE)[3])
12+
ulimit::memory_limit(memlimit)
13+
print(master)
14+
print(memlimit)
15+
has_pryr = requireNamespace("pryr", quietly=TRUE)
16+
17+
library(rzmq)
18+
context = init.context()
19+
socket = init.socket(context, "ZMQ_REQ")
20+
connect.socket(socket, master)
21+
send.socket(socket, data=list(id=0, worker_id=worker_id))
22+
msg = receive.socket(socket)
23+
fun = msg$fun
24+
const = msg$const
25+
seed = msg$seed
26+
27+
print(fun)
28+
print(names(const))
29+
30+
start_time = proc.time()
31+
counter = 0
32+
33+
while(TRUE) {
34+
msg = receive.socket(socket)
35+
if (identical(msg$id, 0))
36+
break
37+
38+
one_id = function(seq_num) {
39+
set.seed(seed + msg$id[seq_num])
40+
result = try(do.call(fun, c(const, msg$iter[[seq_num]])))
41+
}
42+
result = lapply(seq_along(msg$id), one_id)
43+
counter = counter + length(msg$id)
44+
45+
send.socket(socket, data=list(id = msg$id, result=result))
46+
47+
if (has_pryr)
48+
print(pryr::mem_used())
49+
}
50+
51+
run_time = proc.time() - start_time
52+
53+
send.socket(socket, data=list(id=-1, worker_id=worker_id, time=run_time, calls=counter))
54+
55+
print(run_time)
56+
}

‎worker.r

-49
This file was deleted.

0 commit comments

Comments
 (0)