[Question] Is Linux ARM64 a supported architecture?

2022-07-20T11:16:02.445000Z

Hello,

I’d like to ask whether HipMer is supported on Linux/Mac ARM64 systems ?
Any concerns ?
Any positive/negative experience ?

Thank you!

Installation error posix/dbg_cupc2c

2020-09-15T18:21:52.801000Z

My OS is Ubuntu 18.04 running in a virtual machine. Both gcc 4.8 and 7.5 are installed.

Installation error posix/dbg_cupc2c

2020-09-15T18:20:32.062000Z

Hi authors!

I tried installing Hipmer and I am getting the following error

       === Multiconf configuring: dbg_cupc2c ===

Configuring Berkeley UPC Runtime version 2020.4.0 with the following options:
--with-clang-upc2c=posix/bin/clang-upc2c --enable-debug --with-multiconf=+dbg_cupc2c,+opt_cupc2c --enable-pthreads --enable-udp --enable-smp --with-default-network=contrib/install_upc.sh --enable-sptr-struct --disable-sptr-struct --with-sptr-packed-bits=10,18,36 --prefix=posix/dbg_cupc2c --with-multiconf-magic=dbg_cupc2c
configure: error: expected an absolute directory name for --prefix: posix/dbg_cupc2c
Failed during dbg_cupc2c configure, exit=1
+ set -x
+ trap '' 0

I tried following commands and both gave me the same error.

contrib/install_upc.sh contrib/install_upc.sh ivb posix [install_path=/home/baadalvm/install]

contrib/install_upc.sh contrib/install_upc.sh smp posix [install_path=/home/baadalvm/install]

Trim and Merge Output

2019-04-18T00:45:01.622000Z

Thanks Eugene. That sounds easy enough!

Trim and Merge Output

2019-04-17T21:59:19.237000Z

In this version you can treat them as different libraries, i.e. make two lib_seq entries for each file and give different library names, but assign the same setID of 1 so that they're used together for scaffolding. You can enter the same insert size/sdev for both - the pipeline will recalculate it later anyway, so these are treated as just fallback estimates.
In the next release all this will be handled automatically.
Hope this helps.

Trim and Merge Output

2019-04-17T17:41:54.609000Z

Dear all,
I have adapted the trim and merge script in the contrib folder and applied to my dataset. The output includes a merged file and a pairs file. My question is, should I feed thee two files as two different libraries to Hipmer? Or do they count as a single library?

The results outputed by the script include the avg insert and its standard deviation... is that for the merged file? can I use those reported numbers as input in the meraculous config file?

Thanks for the clarification.

Running out of memory at stage contigMerDepth_main

2019-04-16T16:22:18.109000Z

Hello all!

I am running hipmer on a plant data set. Hipmer runs fine until it is killed by slurm for trying to exceed the physical memory available in my compute nodes. The final part of the run.out file is as so:

Starting stage contigMerDepth-31 -k 31 -i ALL_INPUTS.fofn-31.ufx.bin -c UUtigs_contigs-31 -d 7 -D 1.000000 -s 100 -B /dev/shm at 04/16/19 10:52:31

STAGE contigMerDepth_main -k 31 -i ALL_INPUTS.fofn-31.ufx.bin -c UUtigs_contigs-31 -d 7 -D 1.000000 -s 100 -B /dev/shm
Struct size is 32, no padding, 8 shared[] ptr
kmer_length 31
Total number of records is 1027287713
Minimum required shared memory: 279 MB. (1027287713 ufx kmers) If memory runs out re-run with more -shared-heap
Thread 0: Allocating memory for 6111570 reads: 281132220 bytes
Threads done with I/O
Time spent in all_alloc() for buckets is 0.081163 seconds
Time spent in NULL-ing buckets is 0.078106 seconds
Time spent in all_alloc() for heap ptrs and indices is 0.001610 seconds
Time spent in alloc() for my shared heap is 0.087445 seconds
Allocating 31.500 MB per node 256 elements (32 bytes) per-thread for local chunks
Time spent for caching remote pointers is 0.010392 seconds
Threads done with setting-up

**** SET - UP TIME **
Time spent on setting up the distributed hash table is 0.616881 seconds

** OVERALL TIME BREAKDOWN **

Time for constructing UFX hash table is : 10.879285 seconds

My standard error file has in additions this:

slurmstepd: error: Job 9523 exceeded memory limit (97778864 > 97320960), being killed
slurmstepd: error: Exceeded job memory limit
slurmstepd: error: JOB 9523 ON node06 CANCELLED AT 2019-04-16T10:52:59

The end of the output clearly states that if I run out of memory, I should run with more shared-heap. How exactly does that work? It seems that hipmer was allocating more memory than available in a single node, so I don't see how increasing the shared-heap would help.

Is my problem a different one, could I improve on this situation by increasing the number of nodes (and therefore the available memory)? Or are there steps within hipmer where the memory cannot be distributed? I could answer this questions myself by running on more nodes, but it will be a while until those are available in my cluster, so wanted to get a head-start for planning.

Thanks for your help!

long runtime in merAligner

2017-08-22T16:12:23.266000Z

Hello there!

I have been trying to run a large wheat input on a large cluster system, and I have gotten as far as running it to completion using ~1000 cores, but with ~3000 cores it appears to be stuck trying to get through merAligner-51. It looks like there is probably some contention for some shared resources, but I was wondering if you might have any insights or suggestions as to what might be going on and what I might try next.

I built UPC/GASnet with --disable-shmem --with-sptr-packed-bits=20,12,32, and I am using the Intel compilers and SGI MPT for MPI. I have run HipMer (built using UPCC_FLAGS="-network mpi") with UPC_SHARED_HEAP_MB ranging from 800MB to 3000MB. My configuration file looks like this:

$ cat meraculous-cs42.config

lib_seq R1.fastq,R2.fastq CS42 1000 150 251 1 1 1 1 1 0 0 2 1

is_diploid 0
genome_size 13
mer_size 51
min_depth_cutoff 0
gap_close_rpt_depth_ratio 1.75
gap_close_aggressive 1

Thank you so much!!

-- Haruna :)

install error of HipMer~

2017-02-23T09:16:04.616000Z

Hello, we can't replicate this bug, and it seems to indicate that there is an issue with your version of glibc.

Please open a ticket and include your full build log and the OS, version and patch level of the machine you are building on. We have primarily been testing on Ubuntu 16.04, and SLE6 (Cray), so there may be issues with other flavors of Linux that we have not come accross.

install error of HipMer~

2017-02-22T11:15:42.134000Z

I am using gcc 4.9.0, sorry for late

Recent posts to Discussion

[Question] Is Linux ARM64 a supported architecture?

Installation error posix/dbg_cupc2c

Installation error posix/dbg_cupc2c

Trim and Merge Output

Trim and Merge Output

Trim and Merge Output

Running out of memory at stage contigMerDepth_main

long runtime in merAligner

install error of HipMer~

install error of HipMer~