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Oliver Perks
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Merge pull request #46 from sub-rat/app/amg2013
App/amg2013
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Applications/Applications/amg2013/README.md

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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**URL:** https://computing.llnl.gov/projects/co-design/amg2013
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**Team:**
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**Team:** HPCNepal
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## Compilation
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@@ -20,23 +20,163 @@ Pull request for Spack recipe changes:
2020

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#### Compiler 1
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#### gcc 10.3.0
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```
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spack install <app>%<compiler1>
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spack install amg2013%[email protected]
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```
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```
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$ spack spec -Il <app>%<compiler1>
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$ spack spec -Il amg2013%[email protected]
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```
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```
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Input spec
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--------------------------------
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Concretized
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--------------------------------
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[+] twfpbbe amg2013@master%[email protected]~assumedpartition~int64+openmp arch=linux-amzn2-graviton2
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[+] zvamksn ^[email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8 schedulers=slurm arch=linux-amzn2-graviton2
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[+] cukmqbg ^[email protected]%[email protected]~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-graviton2
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[+] asgtk6a ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] z2uysov ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] ebhjpix ^[email protected]%[email protected]+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-graviton2
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[+] ltbv6bk ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] s4pw7zm ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] 4xr3hhh ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] iyhm3wi ^[email protected]%[email protected]~python arch=linux-amzn2-graviton2
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[+] y5ei3cm ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] ye3kcvv ^[email protected]%[email protected]~pic libs=shared,static arch=linux-amzn2-graviton2
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[+] qepjcvj ^[email protected]%[email protected]+optimize+pic+shared arch=linux-amzn2-graviton2
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[+] iwzirqc ^[email protected]%[email protected]~symlinks+termlib abi=none arch=linux-amzn2-graviton2
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[+] tadxrfp ^[email protected]%[email protected]+openssl arch=linux-amzn2-graviton2
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[+] 5i3lgfb ^[email protected]%[email protected]~docs+systemcerts arch=linux-amzn2-graviton2
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[+] 4m7exgb ^[email protected]%[email protected]+cpanm+shared+threads arch=linux-amzn2-graviton2
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[+] y42m6yr ^[email protected]%[email protected]+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-graviton2
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[+] rqrpmap ^[email protected]%[email protected]~debug~pic+shared arch=linux-amzn2-graviton2
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[+] 2w7bert ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] wjwqncx ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] 3zy7kxk ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] 72f5gvk ^[email protected]%[email protected]~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-graviton2
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[+] mhav5gn ^[email protected]%[email protected] patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-graviton2
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[+] jkuhz64 ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] xb2w5nc ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] wturp6c ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] ivotdt7 ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] wqpuvmh ^slurm@20-02-4-1%[email protected]~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-graviton2
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```
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#### arm 21.0.0.879
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```
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spack install amg2013%[email protected]
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```
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```
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$ spack spec -Il amg2013%[email protected]
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```
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```
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Input spec
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--------------------------------
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Concretized
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--------------------------------
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==> Warning: [email protected] cannot build optimized binaries for "graviton2". Using best target possible: "aarch64"
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[+] q6x6lzj amg2013@master%[email protected]~assumedpartition~int64+openmp arch=linux-amzn2-aarch64
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[+] lmaoy5t ^[email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8 schedulers=slurm arch=linux-amzn2-aarch64
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[+] xl6anaa ^[email protected]%[email protected]~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-aarch64
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[+] jueqz7p ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] e4ssqx6 ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] i2jmeo4 ^[email protected]%[email protected]+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-aarch64
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[+] 6jhzlul ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] zpuzm23 ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] uwcxkin ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] dypqz2i ^[email protected]%[email protected]~python arch=linux-amzn2-aarch64
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[+] 7vnthzn ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] zqsab4f ^[email protected]%[email protected]~pic libs=shared,static arch=linux-amzn2-aarch64
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[+] puuxvg2 ^[email protected]%[email protected]+optimize+pic+shared arch=linux-amzn2-aarch64
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[+] uhtqtlb ^[email protected]%[email protected]~symlinks+termlib abi=none arch=linux-amzn2-aarch64
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[+] gonqskn ^[email protected]%[email protected]+openssl arch=linux-amzn2-aarch64
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[+] vc3waha ^[email protected]%[email protected]~docs+systemcerts arch=linux-amzn2-aarch64
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[+] vv6txro ^[email protected]%[email protected]+cpanm+shared+threads arch=linux-amzn2-aarch64
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[+] 33wiajj ^[email protected]%[email protected]+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-aarch64
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[+] z4ybgri ^[email protected]%[email protected]~debug~pic+shared arch=linux-amzn2-aarch64
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[+] adtc6yc ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] 645q4qj ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] 3haw5gt ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] qdn27nh ^[email protected]%[email protected]~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-aarch64
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[+] mv2g7r5 ^[email protected]%[email protected] patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-aarch64
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[+] dcs645r ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] edezkz3 ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] 6vvthuo ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] xe4evc4 ^[email protected]%[email protected] arch=linux-amzn2-aarch64
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[+] x5xehti ^slurm@20-02-4-1%[email protected]~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-aarch64
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```
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```
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spack install amg2013%[email protected]
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```
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```
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$ spack spec -Il amg2013%[email protected]
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```
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```
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Input spec
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--------------------------------
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Concretized
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--------------------------------
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[+] eiqymzo amg2013@master%[email protected]~assumedpartition~int64+openmp arch=linux-amzn2-graviton2
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[+] krxyvbc ^[email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8,fba0d3a784a9723338722b48024a22bb32f6a951db841a4e9f08930a93f41d7a schedulers=slurm arch=linux-amzn2-graviton2
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[+] jroqews ^[email protected]%[email protected]~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-graviton2
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[+] e4m4ued ^[email protected]%[email protected] patches=6e08dc445ece06e9e8b1344397f2d3f169005703ddc0f2ae24f366cde78c7377 arch=linux-amzn2-graviton2
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[+] kk4ax3i ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] 6c4kz5g ^[email protected]%[email protected]+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,5746cf51f45b405661c3edae7a78c33d41e54d83f635d16e2bf1f956dbfbf635,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-graviton2
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[+] pa6wm5j ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] vtiml6g ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] 4imdwuy ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] wo4l72s ^[email protected]%[email protected]~python patches=05ff238cf435825ef835c7ae39376b52dc83d8caf19e962f0766c841386a305a,10a88ad47f9797cf7cf2d7d07241f665a3b6d1f31fa026728c8c2ae93e1664e9 arch=linux-amzn2-graviton2
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[+] r7mmkdp ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] br733tn ^[email protected]%[email protected]~pic libs=shared,static arch=linux-amzn2-graviton2
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[+] 4js6ect ^[email protected]%[email protected]+optimize+pic+shared arch=linux-amzn2-graviton2
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[+] asgm7mt ^[email protected]%[email protected]~symlinks+termlib abi=none arch=linux-amzn2-graviton2
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[+] uttaumr ^[email protected]%[email protected]+openssl arch=linux-amzn2-graviton2
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[+] j2qhi7h ^[email protected]%[email protected]~docs+systemcerts arch=linux-amzn2-graviton2
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[+] gn4fgp5 ^[email protected]%[email protected]+cpanm+shared+threads patches=21cf6a73cec16760f8de2e8895ace1299aff2d8e92dc581cd18f1d95a4503048 arch=linux-amzn2-graviton2
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[+] 5uyf3k4 ^[email protected]%[email protected]+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-graviton2
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[+] wsi7g3j ^[email protected]%[email protected]~debug~pic+shared arch=linux-amzn2-graviton2
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[+] s4mb5no ^[email protected]%[email protected] patches=6e42dc243f17aab29fd167f060f5bc1f08813e03368eb301b43c95d4b1386681 arch=linux-amzn2-graviton2
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[+] m2wdbeo ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] zori3wf ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] xl6zavq ^[email protected]%[email protected]~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-graviton2
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[+] 5yq4tpw ^[email protected]%[email protected] patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-graviton2
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[+] fo57byt ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] gmd4264 ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] cl3ohqo ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] yvqpq74 ^[email protected]%[email protected] arch=linux-amzn2-graviton2
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[+] zehhooy ^slurm@20-02-4-1%[email protected]~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-graviton2
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```
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## Test Case 1
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## Test Case
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[ReFrame Benchmark 1](#)
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```
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../bin/reframe -c benchmark.py -r --performance-report
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../bin/reframe -c amg2013_short.py -r --performance-report
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```
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### Validation
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==============================================================================
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PERFORMANCE REPORT
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------------------------------------------------------------------------------
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****
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_1
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- aws:c6gn
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- builtin
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* num_tasks: 1
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* Total Time: 1848879.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_2
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- builtin
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* num_tasks: 1
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* Total Time: 2640431.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_4
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- builtin
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* num_tasks: 1
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* Total Time: 3499481.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_8
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- builtin
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* num_tasks: 1
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* Total Time: 3551646.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_16
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- builtin
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* num_tasks: 1
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* Total Time: 2584852.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_32
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- builtin
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* num_tasks: 1
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* Total Time: 1513061.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__gcc_10_3_0_N_1_MPI_1_OMP_64
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- builtin
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* num_tasks: 1
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* Total Time: 830065.2 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_1
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- builtin
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* num_tasks: 1
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* Total Time: 1702493.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_2
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- builtin
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* num_tasks: 1
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* Total Time: 2134396.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_4
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- builtin
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* num_tasks: 1
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* Total Time: 2906109.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_8
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- builtin
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* num_tasks: 1
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* Total Time: 2793329.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_16
250+
- builtin
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* num_tasks: 1
252+
* Total Time: 2597610.0 s
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------------------------------------------------------------------------------
254+
amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_32
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- builtin
256+
* num_tasks: 1
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* Total Time: 2092261.0 s
258+
------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__arm_21_0_0_879_N_1_MPI_1_OMP_64
260+
- builtin
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* num_tasks: 1
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* Total Time: 1628985.0 s
263+
------------------------------------------------------------------------------
264+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_1
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- builtin
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* num_tasks: 1
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* Total Time: 1765272.0 s
268+
------------------------------------------------------------------------------
269+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_2
270+
- builtin
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* num_tasks: 1
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* Total Time: 2285842.0 s
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------------------------------------------------------------------------------
274+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_4
275+
- builtin
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* num_tasks: 1
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* Total Time: 3051910.0 s
278+
------------------------------------------------------------------------------
279+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_8
280+
- builtin
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* num_tasks: 1
282+
* Total Time: 3160689.0 s
283+
------------------------------------------------------------------------------
284+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_16
285+
- builtin
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* num_tasks: 1
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* Total Time: 2496395.0 s
288+
------------------------------------------------------------------------------
289+
amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_32
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- builtin
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* num_tasks: 1
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* Total Time: 1239280.0 s
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------------------------------------------------------------------------------
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amg2013_amg2013_0_amg2013__nvhpc_21_2_N_1_MPI_1_OMP_64
295+
- builtin
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* num_tasks: 1
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* Total Time: 487107.5 s
54298
------------------------------------------------------------------------------
55299
```
56300

57301
### On-node Compiler Comparison
58302

59303
Performance comparison of two compilers.
60-
61-
| Cores | Compiler 1 | Compiler 2 |
62-
|-------|------------|------------|
63-
| | | |
64-
65-
304+
```
305+
| Cores(OMP rank) | GCC | ARM | NVHPC|
306+
|--------|------------|------------|
307+
| 1 | 10.295 | 7.300 | 19.736 |
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| 2 | 9.551 | 26.67 | 18.709 |
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| 4 | 8.805 | 25.239 | 16.558 |
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| 8 | 8.450 | 22.822 | 17.390 |
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| 16 | 9.473 | 7.812 | 12.429 |
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| 32 | 6.992 | 279.186| 276.317 |
313+
| 64 | 281.773 | 9.072 | 12.124 |
314+
```
66315
### Serial Hot-spot Profile
67316

68317
List of top-10 functions / code locations from a serial profile.
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@
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import reframe as rfm
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import reframe.utility.sanity as sn
3+
import hackathon as hack
4+
5+
@rfm.simple_test
6+
class Amg2013Test(hack.HackathonBase):
7+
# Where to run the binaries 'aws:c6gn' on Arm or 'aws:c5n' on Intel
8+
valid_systems = ['aws:c6gn']
9+
10+
# Logging Variables
11+
log_team_name = 'HPCNepal'
12+
log_app_name = 'amg2013'
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log_test_name = 'amg2013_0'
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# Define test case
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# In this case we download the file from GitHub and write as clover.in - the expected input file
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prerun_cmds = ["wget https://asc.llnl.gov/sites/asc/files/2021-01/amg2013_0.tgz","tar xzf amg2013_0.tgz"]
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# Define Execution
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# Binary to run
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executable = 'amg2013'
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# Command line options to pass
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executable_opts = ['-in', './AMG2013/test/sstruct.in.MG.FD']
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# Where the output is written to
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logfile = 'amg2013.out'
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# Store the output file (used for validation later)
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keep_files = []
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# Parameters - Compilers - Defined as their Spack specs (use spec or hash)
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spec = parameter([
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'amg2013 %[email protected]', # MiniTri with the GCC compiler
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'amg2013 %[email protected]', # MiniTri with the Arm compiler
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'amg2013 %[email protected]' # MiniTri with the NVIDIA compiler
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])
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parallelism = parameter([
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 1},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 2},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 4},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 8},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 16},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 32},
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{ 'nodes' : 1, 'mpi' : 1, 'omp' : 64},
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])
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@run_before('run')
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def prepare_job(self):
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self.job.options += ['--exclusive=user']
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self.job.launcher.options = ['time']
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# Code validation
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@run_before('sanity')
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def set_sanity_patterns(self):
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# Use the logfile for validation testing and performance
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# Regex - Number of Iterations
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sol_regex = r'Final Relative Residual Norm = (\S+)'
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# Validate for Relative Residual Norm (1)
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no_of_final_rrn_count = sn.extractsingle(sol_regex, self.stdout, 1, float)
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expected_upper = 1
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expected_lower = 0
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# Perform a bounded assert
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self.sanity_patterns = sn.assert_bounded(no_of_final_rrn_count,expected_lower, expected_upper)
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# Performance Testing - FOM Total Time units 's'
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# We dont set an expected value
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self.reference = {
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'*': {'Total Time': (0, None, None, 's'),}
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}
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pref_regex = r'System Size \* Iterations \/ Solve Phase Time: (\S+)'
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self.perf_patterns = {
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'Total Time': sn.extractsingle(pref_regex, self.stdout, 1, float, item=-1)
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}

Tutorials/CloverLeaf/cloverleaf_bm16_short.py

-1
Original file line numberDiff line numberDiff line change
@@ -76,4 +76,3 @@ def set_sanity_patterns(self):
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self.perf_patterns = {
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'Total Time': sn.extractsingle(perf_regex, self.logfile, 1, float, item=-1)
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}
79-

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