A Data-Aware MultiWorkflow Cluster Scheduler
esar Acevedo, Porfidio Hern
andez, Antonio Espinosa and Victor M
Computer Architecture and Operating System, Univ. Aut
onoma de Barcelona, Barcelona, Spain
Multiple, Multiworkflows, Data-Aware, Cluster.
Previous scheduling research work is based on the analysis of the computational time of application workflows.
Current use of clusters deals with the execution of multiworkflows that may share applications and input files.
In order to reduce the makespan of such multiworkflows adequate data allocation policies should be applied to
reduce input data latency. We propose a scheduling strategy for multiworkflows that considers the data location
of shared input files in different locations of the storage system of the cluster. For that, we first merge all
workflows in a study and evaluate the global design pattern obtained. Then, we apply a classic list scheduling
heuristic considering the location of the input files in the storage system to reduce the communication overhead
of the applications. We have evaluated our proposal with an initial set of experimental environments showing
promising results of up to 20% makespan improvement.
Scheduling a workflow with precedence constraints is
an important problem in scheduling theory and has
been shown to be NP-Hard (Pinedo, 2012). There
are many studies on how to schedule a single work-
flow, specially when trying to schedule tasks onto het-
erogeneous domains (Topcuoglu et al., 1999). There
is an increasing interest in executing several work-
flows simultaneously. The problem of defining which
application from the multiple workflows is going
to be executed in a specific node of a cluster, has
been described in several works like (Bittencourt
and Madeira, 2010), (Stavrinides and Karatza, 2011),
(Zhao and Sakellariou, 2006), (H
onig and Schiff-
mann, 2006), (Yu and Shi, 2008), (N’Takp
e and Suter,
2009), (Afrati et al., 1988), (Rahman et al., 2007),
(Gu and Wu, 2010).
Current scientific applications must deal with
large data sets, usually demanding large amounts of
computation and communication times. In many
cases, systems undergo undesired idle times between
data transfers and application execution (Stavrinides
and Karatza, 2011). Our proposal is to make use
of these idle times between scheduled tasks with bin
packing techniques with a list scheduling approach.
Workflow-aware storage is the key to select the lo-
cation of the data as relevant criteria for the applica-
tion scheduling. This idea has previously been used
to reduce the I/O load of a cloud system (Wang et al.,
We present on figure 1 a simple scenario where a
scheduler needs to decide for one workflow the need
of locating input, temporal and output data files on the
hierarchical storage system. If we extend the problem
to multiworkflows to reduce the data access latency,
we need to resolve some issues. If an input or tempo-
ral files are going to be read several times by many ap-
plications at a given time and the cost of reading once
from a distributed file system and writing on a local
disk or local memory of the computing node is low;
then we need to store locally these data files previous
to the execution. We will need to manage files when a
local storage is full and define where to locate output
files if they are final results on to distributed file sys-
tem to avoid using critical space on smaller storage
systems (Costa et al., 2015).
Figure 1: Data location of workflow scheduling.
Acevedo, C., Hernandez, P., Espinosa, A. and Méndez, V.
A Data-Aware MultiWorkflow Cluster Scheduler.
In Proceedings of the 1st International Conference on Complex Information Systems (COMPLEXIS 2016), pages 95-102
ISBN: 978-989-758-181-6
2016 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved
Executing multiples workflows exposes another
problem for distributed file systems like Lustre. Tra-
ditionally it is difficult to predict performance on
shared High Performance Computing environments
(Zhao and Hu, 2010). Applying special techniques
on access optimization (Meswani et al., 2010) is
also complicated. Therefore we have decided to use
”share nothing” nodes or storage hierarchies where
predictability index is better such as local file systems
or Ramdisk.
Due to the peculiarity of bioinformatics work-
flows that are composed of many applications that
share files, we can take advantage of reading a cached
file. An extension of the classic model of execution
and mapping of workflow application of this kind of
architecture to a Shared Input File policy is proposed.
The amount of data needs to be taken into account on
the specifications of the abstract graph of the work-
flow to exploit hierarchical storage systems.
In this paper, we propose a scheduling algorithm
for multiworkflows in a cluster environment.
We propose to evaluate the rendering pattern of
the workflow and analyze a list of attributes from it.
We are considering input and output data size and lo-
cation, branch and depth factors for each workflow.
Then we apply a storage-aware mechanism to reduce
the cost of I/O operations of the system. For that,
we analyze shared input files in the storage hierar-
chy and merge workflows in a study into a new meta-
workflow. We apply critical path analysis to reduce
the makespan of multiworkflows.
This approach has been evaluated with an initial
set of experimental environments. With classic List
Scheduling with NFS as the storage system and List
Scheduling for data-aware multiworkflows using a lo-
cal disk. Another experimental scenario with List
Scheduling and local disk and ramdisk for the data-
aware approach. The last experiment with shared in-
put file of 2 files with sizes of 2048Mb, 1024Mb, and
512Mb. The promising initial results show that our
scheduler improves makespan in up to 20%.
The rest of the paper is organized as follows. Re-
lated work is discussed in Section II. Then we de-
scribe the scheduler architecture in Section III. Sec-
tion IV elaborates the experiment design and eval-
uates the performance of proposed algorithm along
with other versions. Finally, we summarize and lay
out the future work in Section V.
Prior research focuses on scheduling heuristics for
single workflow (Kwok and Ahmad, 1999) provides
the taxonomy of approaches that classifies static al-
gorithms according to functionalities. Clustering ap-
proaches reduce communication costs by grouping
applications with high communication cost into a
cluster (Yang and Gerasoulis, 1994). Duplication
heuristic (Park et al., 1997) provides a method for
an application to transmit data to succeeding appli-
cations creating duplicate applications on the destina-
tion compute node or processor. Level based method
divides workflows into independent applications lev-
els and then apply the map of applications to re-
sources (Mandal et al., 2005).
List scheduling algorithms (Ilavarasan and Tham-
bidurai, 2007) try to implement low complexity
heuristics for heterogeneous environments. Other al-
ternatives (Bolze et al., ) minimize the makespan of
the workflow, providing a sorted list of applications
according to their prioritization such as Critical Path
(Topcuoglu et al., 1999).
A method to schedule multiworkflow (Barbosa
and Monteiro, 2008) uses list scheduling heuristic
maximizing the resource usage by assigning a vari-
able amount of resources to an application instead
of a fixed set of resources. Also, (Bittencourt and
Madeira, 2010) provides a path clustering heuris-
tic with 4 different application orders to be submit-
ted, like sequential, gap search, interleave and graph
groups methods.
However, for list scheduling, not much research
has been done that takes into account that many ap-
plications have evolved from compute-intensive to
data-intensive. Neither workflow-aware scheduling as
(Costa et al., 2015) that provides methods to expose
data location information that generally are hidden to
exploit a per-file access optimization. The next step
to data location research has been done. Some exam-
ples like PACman (Ananthanarayanan et al., 2012),
RamCloud (Ousterhout et al., 2011), and RamDisk
(Wickberg and Carothers, 2012) provide data location
techniques but not all of them in a cluster-based envi-
ronment. When these applications are from scientific
field, input files are shared by many of them. CoScan
(Wang et al., 2011) studies how caching input files im-
proves execution time when several applications are
going to read the same information.
In order to expose the information about data loca-
tion of multiworkflows, we need to have a global view
of it. For (Zhao and Sakellariou, 2006) and (H
and Schiffmann, 2006) a meta-scheduler for multiple
DAGs shows a way of merging multiple workflows
into one, to improve the overall parallelism. Expose
the information about data location would be easier to
implement on list scheduling heuristics previous to a
scheduling stage.
COMPLEXIS 2016 - 1st International Conference on Complex Information Systems
A scientific workflow scheduling taxonomy has
been presented by (Yu and Buyya, 2005) with clas-
sification and characterization of various approaches.
For high-level features to aid in a coherent description
of workflow logic and design (flow-charting, logical
diagramming, template write down, among others).
More recently (Cerezo et al., 2013), the same de-
sign principle opened to disaggregated systems be-
tween the abstract layer and the concrete layer. In
the abstract layer, the workflow parallelization possi-
bilities are described in a declarative way. The actual
execution and distribution of the jobs are managed at
the concrete level. A list based scheduling heuristic
could be applied on the meta-workflow with a policy
to cache shared input files and temporal files. In order
to improve the access latency to data a storage hierar-
chy as a local disk and local ramdisk of the compute
node is used.
For our proposal, we try to fit a data-aware mul-
tiworkflows scheduling in a cluster environment. Se-
lecting a list-based scheduling implemented with an
abstract meta-workflow model. We supply to our
scheduler with information about computation time,
data location, sizes and shared input files to reduce
data access latency on the storage hierarchy.
A representative characterization of real workflows
structures composed by bioinformatics applications
as showed on figure 2 is introduced here. We can see
that the reference file is a shared input for two differ-
ent applications; moreover, we realize that applica-
tions executed in the cluster are from workflows used
for genome alignment, variant analysis, and data file
format transformation. We select 4 of the most rep-
resentative bioinformatics applications; seen in table
Reads File
Data File
Shared Input
Figure 2: Shared input bioinformatics workflow.
Table 1: Workflow applications considered.
Applications Bound Objective
Fast2Sanger I/O Format Transformation
BWA CPU Alignment
Sam2Bam I/O Format Transformation
Gatk CPU Variant Analysis
As shown in figure 3, based on the type of bioin-
formatics research executed in the cluster, we define
that there are two main patterns of execution: sequen-
tial and parallel branch applications.
Data File
Figure 3: Bioinformatics workflow patterns.
These applications take as input data files with dif-
ferent sizes. We classify files as small when they are
below 1 MB, medium below 1 GB and big above 1
GB. Our first approach is to implement a data locality
policy and avoid a complete statistical analysis of all
possible combinations for locating a file in the differ-
ent levels of the hierarchy: distributed file system on
NFS, a local disk and a local ramdisk of a computa-
tional node.
For practical purpose, modules are designed as
shown in figure 4. Different workflows from differ-
ent users could coexist on the system at once. In the
prescheduling stage, we will evaluate the attributes of
the workflow pattern design received from the user-
level. We expose information needed to perform two
main operations; first we merge all applications from
the studied workflows into a single meta workflow
to evaluate a priority list according to a critical path
based heuristic using computation time. Second, with
the information exposed from merging the applica-
tions of the workflows, we know how many applica-
tions are using the same data file as shared input. With
this information about shared input files, we use lo-
cal ramdisk, local hard disk or distributed file system
as target locations in the hierarchical storage system
to allocate them. At last, at the scheduler level, we
use the priority list to assign the highest application
A Data-Aware MultiWorkflow Cluster Scheduler
to a queue of a specific node of the cluster. For these
assignments, we consider which node holds the data
input for those applications.
Figure 4: Scheduler architecture design.
With these specifications we propose an architec-
ture model show in figure 5 for our scheduler. Model
is composed by four main modules: the App Con-
troller, Data Placement, App Scheduling and the Re-
source Status.
App Controller all workflows analysed
through the workflow API are merged into one
meta workflow. Applications in the workflow are
scheduled according to the application computa-
tion time and communication time log stored in
the workflow engine. This information has previ-
ously been selected and categorized. Then, based
on the critical path priorities, we build a list of ap-
plications using algorithm 1.
Data Placement at the very begining input
datasets are located in the distributed file system
and copied to the local disk of the cluster node
where the entry applications are going to be ex-
ecuted. All temporal data files produced by the
applications for next workflow stages should be
stored in the same local disk or Ramdisk. Ac-
cordingly with algorithm 1, if the computational
capacity of the node is full, a copy of the required
data file will be issued in order to start the execu-
tion of the next applications of the workflow in a
different node. This is done to ensure data inde-
pendence between applications in different nodes
and these file copy operations are kept in a list of
data locations.
User Level
User Submit WF
App Status Notification
Node N / Master
Figure 5: Scheduler architecture modules.
In the pre scheduling stage algorithm 1 from lines
1 to 3 we initialize values for the workflow charac-
terization provided by user definition. Lines 5 to
13 merge all workflows into one meta-workflow
adding 2 dummy nodes for start and end nodes.
Following line 14 applies a critical path to this
new meta-workflow. Data placement implemen-
tation is described from line 15. Here we clas-
sify data files as small, which are kept in the dis-
tributed file system. Also, which big or medium
shared files need to be copied to the local storage
system. In line 27, we describe a file replacement
policy when local storage locations are full. In
those cases, we need to copy data files back to the
distributed file system to free storage space. Fi-
nally, in line 40, we describe how all output files
are going to be written into the NFS file system.
All these modules work on a master node of the
Resource Status the status of the resources
and the implementation of some sub-modules are
done with the help of scripts provided by the WF
Engine and systems call to the DRM to retrieve
and send information and instructions to the clus-
COMPLEXIS 2016 - 1st International Conference on Complex Information Systems
Algorithm 1: Pre Scheduling Stage.
input : New WorkFlow, User WF Characterizations
output: Updated Meta Workflow, List Scheduling
1 for All Applications on New Workflow do
2 User Wf Characterization
3 AppId, weight, fileIn, fileInsize, fileOut, fileOutsize, Parents,
BranchBrothers ;
4 end
5 while New Workflow Applications are not in Meta Workflow do
6 Node add of application from New Workflow to Meta
7 if application of New Workflow is an entry then
8 edge from Start node of Meta Workflow to application of
New Workflow;
9 end
10 if application has not successor then
11 edge from application of New Workflow to End node of
Meta Workflow;
12 end
13 end
14 List = CriticalPath on Meta Workflow;
15 for All Applications on List do
16 if application is new then
17 if fileInSize = SMALL then
18 keep file on Distributed File System;
19 end
20 if (fileInSize = MEDIUM or BIG) and more than 1
application use it then
21 if Ramdisk is not full then
22 copy file input from Distributed File System
to local Ramdisk of Computational Node;
23 end
24 else
25 Replace Input file from Ramdisk;
26 if Replaced file is Temporal and
BranchBrothers are DONE then
27 delete replaced file
28 end
29 else if Local disk is not full then
30 copy replaced input file to Local disk of
Computational Node;
31 end
32 else
33 Replace input file from LocalDisk;
34 copy replaced input file to Distributed
File System;
35 end
36 end
37 end
38 end
39 if FileOut is from Last Application then
40 Copy FileOut to NFS
41 end
42 end
ter. App Executor just submits the first application
of the list provided by the App Controller. Instruc-
tions about which node and resource to use is pro-
vided here to the Distributed Resource Manager
(DRM) so this can schedule at the internal appli-
cation queue. In the meanwhile, the Data Place-
ment use the information provided by the DRM to
move output files to the distributed file system.
App Scheduling – workflows are made of inter-
dependent applications. The scheduler submits an
individual application to the system queue only
when they are ready to execute. The list of ap-
plications is sorted in one unique list of ready ap-
plications. The highest priority application will
be on the top of the list to be mapped to a re-
source and will be sent to the Application Ex-
ecutor when all its parents are done. We apply
a scheduling algorithm to the list of applications
described in algorithm 2. The priority of an ap-
plication can change dynamically while the appli-
cation is not running whether the application be-
longs to different workflows or users. In this first
approach, we do not perform an analysis to se-
lect the exact amount of computational resources
needed; Instead, we limit the maximum selection
to the maximum branch factor of the workflow.
We describe the scheduler module algorithm in 2.
In line 1 we receive resource status from DRMAA
and system calls. Once we have all the information
about resources availability, at line 3 and 4 we sort
the list of priorities and upgrade all applications sta-
tus to STANDBY. We select the resources where to
assign applications in line 5 taking into account the
maximum branch of the workflow where the current
application that is going to submit belongs. From
lines 6 to 17 we make effective the resource assign-
ment. If all parents of the application are DONE, we
move the application to the end of the list to con-
trol the status later. If the status of one of the par-
ents is not DONE, then the application is moved it
to the first position to wait for all precedence to be
checked and resources are free from it. At the end,
from lines 18 to 24 we control if all the applica-
tions are DONE. A stop control upgrading status to
application is performed.
We introduce a experimental design to evaluate the
Multiple Workflow Data-Aware Scheduler. We com-
paratively evaluate our approach against List Schedul-
ing, List Scheduling with Local Ramdisk and Local
Disk storage with Shared Input File in the Cluster.
Cluster specifications are shown on table 3. We use a
A Data-Aware MultiWorkflow Cluster Scheduler
Algorithm 2: Scheduler.
input : Meta Workflow, List Scheduling, Available Resources
1 Available Resources = Resource Status trough DRMAA calls to the
Distributed Resource Management and system calls;
2 while List of Priorities not empty do
3 upgrade application status to STANDBY ;
4 Sort List of Priorities;
5 Select Resources = Max(BranchBrothers of first on List);
6 for i = All Applications in List do
7 if all Parents of application == DONE and Selected
Resources != 0 then
8 if fileInput of Application[i] already on place then
9 execute Application on Selected Resource;
10 Selected Resources = Selected Resources - 1
11 add to List of Priorities at the end;
12 end
13 end
14 else
15 add to List of Priorities at first;
16 end
17 end
18 for all applications in List do
19 if application status is DONE then
20 remove application from List;
21 end
22 upgrade application status to
23 end
24 end
list of well characterized application to test the work-
flow system and then analyze a repository of histori-
cal execution times. We have two workflow patterns
shown in figure 3 with sequential depth factor 8, and
parallel branch factor from 2 to 6. In the table 2 we de-
scribe how many applications are considered in each
pattern. We estimate the execution time using ini-
tial values extracted from NFS application executions.
Cores and CPU speed, as well main memory and local
ramdisk size are shown in table 3 for the 32 compute
nodes and the table 4 for file system specifications.
Table 2: Synthetic workflow specifications.
WorkFlow Applications Exec Time(s)
Sequential 8 480
Branch 8 358
Seq + Branch 4 + 4 360
Table 3: Cluster specifications.
Cores CPU(Ghz) Mem(GB) Ramdisk(GB)
4 2.0 12 6.2
Workflows are constructed with a synthetic set of
applications that simulate the behavior of bioinfor-
matics applications described in table 5, with differ-
Table 4: File System Specs.
LocalRamdisk DistFileSys LocalFileSys
tmpfs nfs ext4
Table 5: Synthetic application specifications.
Apps Exec IO IO RSS(Mb) CPU
Time(s) Read(Mb) Write(Mb) Util(%)
app1 11400 197 304 800 45
app2 1440 67 69 180 98
app3 1020 160 54 480 99
app4 1380 10 47 300 99
ent bounds of CPU and I/O.
We compare here the behavior of the scheduling
algorithm in 3 stages. The Classic List Scheduling
on NFS shows the obtained makespan of using input,
output and temporal files on NFS. Next we have an-
other 2 different implementations of our Multi Work-
flow Data-Aware Scheduler (MWS DA Local Disk)
where all the data sets are located in local disk when
we copy input data sets to the local disk of the node
where the execution would happen. And last schedul-
ing (MWS DA Local Disk + Ramdisk) where Local
Disk and Ramdisk are used, when the input data sets
are placed on the local disk and ramdisk. As we can
see for 8 to 128 cores and 2 files as shared input files
of 2048Mb the algorithm scales very well because the
cost of data read and write is drastically reduced when
we move it to a closer location of the compute node,
see figure 6.
8 16 32 64 128
Classic List Scheduling (NFS)
MWS DA (Local Disk)
MWF DA (Local Disk +
Figure 6: Makespan of 50 workflows on up to 128 cores.
We made different experiments from 8, 16, 64
up to 128 cores with shared input files. There was
no significant performance variation for the different
amount of cores. Figure 7 shows the result of us-
ing 128 cores on 2 shared input files with sizes of
2048Mb, 1024Mb, and 512Mb. The experimenta-
tion shows that for big and medium files makespan
is decreased due to the relocation of files as we are
reducing the number of times we read the same file
from NFS or Local Disk. Nevertheless, for small
files like 512Mb, the scalability does not improve be-
cause reading directly from the distributed file system
is faster than moving data to a new location.
COMPLEXIS 2016 - 1st International Conference on Complex Information Systems
2048 1024 512
Shared Input File Size (Mb)
Classic List Scheduling
MWS DA (Local Disk)
MWF DA (Local Disk +
Figure 7: Makespan of 50 Workflows on 128 cores and dif-
ferent shared input files sizes.
The experiment provides us with some ground
where we can conclude that our algorithm is better in
the case of workflows that share data files in different
levels of the memory hierarchy. Without using local
storage our gain is about 11% for 50 Workflows run-
ning at the same time in a 8 core cluster and almost
20% for 128 cores as we can see in figure 6.
We have studied the state of the art of schedulers for
multiworkflows and their taxonomies, and then focus
our work in the field of data-aware policies for clus-
ters. We concentrate our efforts in studying disk I/O
cluster bottlenecks. We characterize bioinformatics
applications where some of them using same data files
as input. Techniques like shared input files are desir-
able to prevent multiple file reads and to improve the
performance of the system I/O.
We have considered a list of options for data re-
placement polices in ramdisk or local disk. To further
increase efficiency of the policies, we should consider
a better prediction technique of how many nodes, pro-
cessors and cores.
Looking forward, this scheduler is ready to be in-
tegrated it to a real scientific workflow manager like
Galaxy (Goecks et al., 2010) which is a web-based
workflow manager widely used in the bioinformatics
This work has been supported by project number
TIN2014-53234-C2-1-R of Spanish Ministerio de
Ciencia y Tecnolog
ıa (MICINN). This work is co-
founded by the EGI-Engage project (Horizon 2020)
under Grant number 654142.
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COMPLEXIS 2016 - 1st International Conference on Complex Information Systems