Started by timer
Running as SYSTEM
Building in workspace /var/lib/jenkins/jobs/cray-hdf5-parallel-h2ologin4/workspace
[SSH] script:
module load cray-hdf5-parallel
~/bin/myenv.sh
mkdir hdf5-jenkins
cd hdf5-jenkins
rm -rf *
cp ~arnoldg/hdf5/ph5example.c .
cc -v -o ph5example ph5example.c
echo "#!/bin/bash" > hdf5.pbs
echo "#PBS -lnodes=1:ppn=16:xe,walltime=00:05:00 -Nhdf5-p" >> hdf5.pbs
echo "cd ~/hdf5-jenkins" >> hdf5.pbs
echo "aprun -n 2 ~/hdf5-jenkins/ph5example -c > ph5example.out" >> hdf5.pbs
echo "aprun -n 1 hostname > stream-compute-node" >> hdf5.pbs
cat -n hdf5.pbs
MYJOBID=`qsub hdf5.pbs`
echo MYJOBID=$MYJOBID
~/bin/wait_for.sh $MYJOBID
# do some validation
module unload cray-hdf5-parallel
module load cray-hdf5
h5dump ParaEg0.h5
cat ph5example.out
echo "=== JOB RAN ON ==="
cat ~/hdf5-jenkins/stream-compute-node
rm -f ~/hdf5-jenkins/stream-compute-node
[SSH] executing...
mkdir: cannot create directory `hdf5-jenkins': File exists
rm /tmp/pe_15097/ph5example_1.s
/opt/cray/cce/8.4.6/CC/x86-64/lib/ccfe -hc -hcpu=interlagos -D __CRAYXE -D __CRAY_INTERLAGOS -D __CRAYXT_COMPUTE_LINUX_TARGET -hnetwork=gemini -nostdinc -isystem /opt/cray/cce/8.4.6/craylibs/x86-64/include -isystem /usr/include -isystem /opt/cray/cce/8.4.6/CC/x86-64/compiler_include_base/basic -isystem /opt/gcc/4.8.1/snos/include -isystem /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1/include -isystem /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1/include-fixed -D__PEDRVR_GCC_BASE_ACTIVE__ -isystem /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1/include -isystem /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1/include-fixed -isystem /opt/cray/mpt/7.5.0/gni/mpich-cray/8.4/include -isystem /opt/cray/libsci/16.11.1/CRAY/8.3/x86_64/include -isystem /opt/cray/hdf5-parallel/1.10.0/CRAY/8.3/include -isystem /opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/include -isystem /opt/cray/alps/5.2.4-2.0502.9774.31.12.gem/include -isystem /opt/cray/xpmem/0.1-2.0502.64982.5.3.gem/include -isystem /opt/cray/gni-headers/4.0-1.0502.10859.7.8.gem/include -isystem /opt/cray/dmapp/7.0.1-1.0502.11080.8.74.gem/include -isystem /opt/cray/pmi/5.0.10-1.0000.11050.179.3.gem/include -isystem /opt/cray/ugni/6.0-1.0502.10863.8.28.gem/include -isystem /opt/cray/udreg/2.3.2-1.0502.10518.2.17.gem/include -isystem /opt/cray/cce/8.4.6/craylibs/x86-64/pkgconfig/../include -isystem /opt/cray/cce/8.4.6/craylibs/x86-64/pkgconfig/..//include -isystem /usr/local/include -isystem /opt/cray/wlm_detect/1.0-1.0502.64649.2.2.gem/include -isystem /opt/cray/krca/1.0.0-2.0502.63139.4.30.gem/include -isystem /opt/cray-hss-devel/7.2.0/include -hpl=/tmp/pe_15097//pldir -rx8413 -ru84059 -CZ /tmp/pe_15097/ph5example.T -Cx -CX /tmp/pe_15097/ph5example.xml -hdecompile=/mnt/a/u/system/bwjenkins/hdf5-jenkins/ph5example. -S /tmp/pe_15097/ph5example_1.s -hipa3 -ufile_id=1 ph5example.c
/opt/cray/cce/8.4.6/CC/x86-64/lib/optcg /tmp/pe_15097//pldir 1
=== RUNNING /u/system/bwjenkins/bin/myenv.sh ===
HOST=h2ologin4
HOME=/u/system/bwjenkins
SCRATCH=/u/system/bwjenkins/scratch
ls SCRATCH:
mdtest
rmg-spp
rmg-spp-topo
setsm_benchmark
setsm_rsync
SPP-PPM
stripe8
sw_config
SWTools-BWCI
sw_workdir
tests
wrf
wrf-spp
my id:
uid=49294(bwjenkins) gid=16228(BW_System) groups=16228(BW_System),999(login_user),1000(ie_user),1001(hpss_user),1009(swtools),16237(jnd)
Currently Loaded Modulefiles:
1) modules/3.2.10.4
2) eswrap/1.3.3-1.020200.1280.0
3) cce/8.4.6
4) craype-network-gemini
5) craype/2.5.8
6) cray-libsci/16.11.1
7) udreg/2.3.2-1.0502.10518.2.17.gem
8) ugni/6.0-1.0502.10863.8.28.gem
9) pmi/5.0.10-1.0000.11050.179.3.gem
10) dmapp/7.0.1-1.0502.11080.8.74.gem
11) gni-headers/4.0-1.0502.10859.7.8.gem
12) xpmem/0.1-2.0502.64982.5.3.gem
13) dvs/2.5_0.9.0-1.0502.2188.1.113.gem
14) alps/5.2.4-2.0502.9774.31.12.gem
15) rca/1.0.0-2.0502.60530.1.63.gem
16) atp/2.0.4
17) PrgEnv-cray/5.2.82
18) cray-mpich/7.5.0
19) craype-interlagos
20) torque/6.0.4
21) moab/9.1.2-sles11
22) java/jdk1.8.0_51
23) globus/6.0
24) gsissh/7.5p1b
25) xalt/0.7.6.local
26) scripts
27) OpenSSL/1.0.2m
28) cURL/7.59.0
29) git/2.17.0
30) wget/1.19.4
31) user-paths
32) gnuplot/5.0.5
33) darshan/3.1.3
34) cray-hdf5-parallel/1.10.0
/opt/cray/cce/8.4.6/cray-binutils/x86_64-unknown-linux-gnu/bin/as -o /tmp/pe_15097/ph5example_1.o --64 /tmp/pe_15097/ph5example_1.s
rm /tmp/pe_15097/ph5example_1.s
/opt/xalt/0.7.6/sles11.3/bin/ld /usr/lib64//crt1.o /usr/lib64//crti.o /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1//crtbeginT.o /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1//crtfastmath.o /opt/cray/cce/8.4.6/craylibs/x86-64/qc_fastmath.o /opt/cray/cce/8.4.6/craylibs/x86-64/no_mmap.o /tmp/pe_15097/ph5example_1.o -Bstatic -rpath=/opt/cray/cce/8.4.6/craylibs/x86-64 -L /opt/cray/cce/8.4.6/CC/x86-64/lib/x86-64 -rpath=/opt/cray/cce/8.4.6/CC/x86-64/lib/x86-64 -L /opt/gcc/4.8.1/snos/lib64 -rpath=/opt/cray/gcc-libs -L /usr/lib64 -rpath=/usr/lib64 -L /lib64 -rpath=/lib64 -L /opt/cray/dmapp/default/lib64 -L /opt/cray/mpt/7.5.0/gni/mpich-cray/8.4/lib -L /opt/cray/dmapp/default/lib64 -L /opt/cray/mpt/7.5.0/gni/mpich-cray/8.4/lib -L /opt/cray/libsci/16.11.1/CRAY/8.3/x86_64/lib -L /opt/cray/hdf5-parallel/1.10.0/CRAY/8.3/lib -L /sw/xe/darshan/3.1.3/darshan-3.1.3/lib -L /opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64 -L /opt/cray/alps/5.2.4-2.0502.9774.31.12.gem/lib64 -L /opt/cray/xpmem/0.1-2.0502.64982.5.3.gem/lib64 -L /opt/cray/dmapp/7.0.1-1.0502.11080.8.74.gem/lib64 -L /opt/cray/pmi/5.0.10-1.0000.11050.179.3.gem/lib64 -L /opt/cray/ugni/6.0-1.0502.10863.8.28.gem/lib64 -L /opt/cray/udreg/2.3.2-1.0502.10518.2.17.gem/lib64 -L /opt/cray/atp/2.0.4/libApp -L /opt/cray/cce/8.4.6/craylibs/x86-64/pkgconfig/../ -L /usr/local/lib -L /opt/cray/wlm_detect/1.0-1.0502.64649.2.2.gem/lib64 @/sw/xe/darshan/3.1.3/darshan-3.1.3/share/ld-opts/darshan-base-ld-opts -lfmpich -lmpichcxx --start-group -ldarshan -ldarshan-stubs --end-group -lz --no-as-needed -lAtpSigHandler -lAtpSigHCommData --undefined=_ATP_Data_Globals --undefined=__atpHandlerInstall -lpthread -lhdf5_hl_parallel -lrt -lz -ldl -lm -lhdf5_parallel -lrt -lz -ldl -lm -lmpichf90_cray -lrt -lpthread -lugni -lpmi -lsci_cray_mpi_mp -lm -lf -lsci_cray_mp -lmpich_cray -lrt -lpthread -lugni -lpmi -lsci_cray_mp -lcraymp -lm -lpthread -lf -lpgas-dmapp -lfi -lu -lrt -ldmapp -lugni -ludreg -lpthread -lm -lcray-c++-rts -lcraystdc++ -lxpmem -ldmapp -lpthread -ludreg -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lugni -lpthread -lalpsutil -lpthread -lrca -lquadmath -lm -lomp -lcraymp -lpthread -lrt -lcray-c++-rts -lcraystdc++ -lm -lmodules -lm -lfi -lm -lquadmath -lcraymath -lm -lgfortran -lquadmath -lf -lm -lpthread -lu -lrt -lcsup --as-needed -latomic --no-as-needed --whole-archive -ltcmalloc_minimal --no-whole-archive -lstdc++ -lpthread --start-group -lc -lcsup -lgcc_eh -lm -lgcc --end-group -T/opt/cray/cce/8.4.6/craylibs/x86-64/2.23.1.cce.ld -L /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1 -L /opt/cray/cce/8.4.6/cray-binutils/x86_64-unknown-linux-gnu/lib -EL -o ph5example --undefined=__pthread_initialize_minimal /opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1//crtend.o /usr/lib64//crtn.o
rm /tmp/pe_15097/ph5example_1.o
/opt/cray/cce/8.4.6/cray-binutils/x86_64-unknown-linux-gnu/bin/objcopy --remove-section=.note.ftn_module_data ph5example
rm /tmp/pe_15097//ph5example_1.xml.Ttmp
rm /tmp/pe_15097//ph5example.T
rm /tmp/pe_15097//ph5example.xml
rm /tmp/pe_15097//pldir/iline_1
rm /tmp/pe_15097//pldir/gline_1
rm /tmp/pe_15097//pldir/PL_path
rm /tmp/pe_15097//pldir/PL_module_list
rm /tmp/pe_15097//pldir/PL_global_data
rm /tmp/pe_15097//pldir/ph5example_1.inl
rmdir /tmp/pe_15097//pldir
rm /tmp/pe_15097//ph5example.Tfe
rm /tmp/pe_15097//ph5example_1.cif.Ttmp
rmdir /tmp/pe_15097/
1 #!/bin/bash
2 #PBS -lnodes=1:ppn=16:xe,walltime=00:05:00 -Nhdf5-p
3 cd ~/hdf5-jenkins
4 aprun -n 2 ~/hdf5-jenkins/ph5example -c > ph5example.out
5 aprun -n 1 hostname > stream-compute-node
INFO: Job submitted to account: jnc
MYJOBID=10679812.bw
=== RUNNING /u/system/bwjenkins/bin/wait_for.sh ===
Sun Dec 8 03:24:09 CST 2019: waiting for 10679812.bw to finish
Sun Dec 8 03:29:09 CST 2019: waiting for 10679812.bw to finish
qstat: Unknown Job Id Error 10679812.bw
10679812.bw finished
HDF5 "ParaEg0.h5" {
GROUP "/" {
DATASET "Data1" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 24, 24 ) / ( 24, 24 ) }
DATA {
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(0,18): 19, 20, 21, 22, 23, 24,
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(1,13): 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
(2,0): 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213,
(2,13): 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224,
(3,0): 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313,
(3,13): 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324,
(4,0): 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413,
(4,13): 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424,
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(5,13): 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524,
(6,0): 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613,
(6,13): 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624,
(7,0): 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713,
(7,13): 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724,
(8,0): 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813,
(8,13): 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824,
(9,0): 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913,
(9,13): 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924,
(10,0): 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010,
(10,10): 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020,
(10,20): 1021, 1022, 1023, 1024,
(11,0): 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110,
(11,10): 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120,
(11,20): 1121, 1122, 1123, 1124,
(12,0): 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210,
(12,10): 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219, 1220,
(12,20): 1221, 1222, 1223, 1224,
(13,0): 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309, 1310,
(13,10): 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320,
(13,20): 1321, 1322, 1323, 1324,
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(14,10): 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420,
(14,20): 1421, 1422, 1423, 1424,
(15,0): 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510,
(15,10): 1511, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 1520,
(15,20): 1521, 1522, 1523, 1524,
(16,0): 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609, 1610,
(16,10): 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620,
(16,20): 1621, 1622, 1623, 1624,
(17,0): 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709, 1710,
(17,10): 1711, 1712, 1713, 1714, 1715, 1716, 1717, 1718, 1719, 1720,
(17,20): 1721, 1722, 1723, 1724,
(18,0): 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809, 1810,
(18,10): 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818, 1819, 1820,
(18,20): 1821, 1822, 1823, 1824,
(19,0): 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909, 1910,
(19,10): 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1920,
(19,20): 1921, 1922, 1923, 1924,
(20,0): 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
(20,10): 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020,
(20,20): 2021, 2022, 2023, 2024,
(21,0): 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110,
(21,10): 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120,
(21,20): 2121, 2122, 2123, 2124,
(22,0): 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209, 2210,
(22,10): 2211, 2212, 2213, 2214, 2215, 2216, 2217, 2218, 2219, 2220,
(22,20): 2221, 2222, 2223, 2224,
(23,0): 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309, 2310,
(23,10): 2311, 2312, 2313, 2314, 2315, 2316, 2317, 2318, 2319, 2320,
(23,20): 2321, 2322, 2323, 2324
}
}
DATASET "Data2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 24, 24 ) / ( 24, 24 ) }
DATA {
(0,0): 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
(0,18): 19, 20, 21, 22, 23, 24,
(1,0): 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113,
(1,13): 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
(2,0): 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213,
(2,13): 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224,
(3,0): 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313,
(3,13): 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324,
(4,0): 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413,
(4,13): 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424,
(5,0): 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513,
(5,13): 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524,
(6,0): 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613,
(6,13): 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624,
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(10,20): 1021, 1022, 1023, 1024,
(11,0): 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110,
(11,10): 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120,
(11,20): 1121, 1122, 1123, 1124,
(12,0): 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210,
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(19,10): 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1920,
(19,20): 1921, 1922, 1923, 1924,
(20,0): 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
(20,10): 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020,
(20,20): 2021, 2022, 2023, 2024,
(21,0): 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109, 2110,
(21,10): 2111, 2112, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120,
(21,20): 2121, 2122, 2123, 2124,
(22,0): 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209, 2210,
(22,10): 2211, 2212, 2213, 2214, 2215, 2216, 2217, 2218, 2219, 2220,
(22,20): 2221, 2222, 2223, 2224,
(23,0): 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309, 2310,
(23,10): 2311, 2312, 2313, 2314, 2315, 2316, 2317, 2318, 2319, 2320,
(23,20): 2321, 2322, 2323, 2324
}
}
}
}
Parallel test files are:
./ParaEg0.h5
./ParaEg1.h5
--------------------------------
Proc 0: *** testing PHDF5 dataset using split communicators...
--------------------------------
--------------------------------
Proc 1: *** testing PHDF5 dataset using split communicators...
--------------------------------
--------------------------------
Proc 1: *** testing PHDF5 dataset independent write...
--------------------------------
--------------------------------
Proc 0: *** testing PHDF5 dataset independent write...
--------------------------------
--------------------------------
Proc 0: *** testing PHDF5 dataset collective write...
--------------------------------
--------------------------------
Proc 1: *** testing PHDF5 dataset collective write...
--------------------------------
--------------------------------
Proc 1: *** testing PHDF5 dataset independent read...
--------------------------------
--------------------------------
Proc 0: *** testing PHDF5 dataset independent read...
--------------------------------
--------------------------------
Proc 1: *** testing PHDF5 dataset collective read...
--------------------------------
--------------------------------
Proc 0: *** testing PHDF5 dataset collective read...
--------------------------------
===================================
PHDF5 tests finished with no errors
===================================
Application 82525151 resources: utime ~0s, stime ~1s, Rss ~22860, inblocks ~11621, outblocks ~29325
=== JOB RAN ON ===
nid27199
Application 82525203 resources: utime ~0s, stime ~1s, Rss ~22860, inblocks ~19, outblocks ~28
[SSH] completed
[SSH] exit-status: 0
[workspace] $ /bin/sh -xe /tmp/jenkins6527834446535694640.sh
+ scp 'BW_REMOTE:~/hdf5-jenkins/*' /var/lib/jenkins/jobs/cray-hdf5-parallel-h2ologin4/workspace
Finished: SUCCESS
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